Epitopes Related To Coeliac Disease

ABSTRACT

The invention herein disclosed is related to epitopes useful in methods of diagnosing, treating, and preventing coeliac disease. Therapeutic compositions which comprise at least one epitope are provided.

RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.14/630,004, filed Feb. 24, 2015, which is a divisional of U.S.application Ser. No. 13/541,864, filed Jul. 5, 2012, which is acontinuation of U.S. application Ser. No. 11/568,428, filed Jul. 9, 2008and now abandoned, which is a national stage entry of InternationalApplication PCT/GB05/01621, filed Apr. 28, 2005, which claims benefit ofAustralian application number 2005900650, filed Feb. 11, 2005 andAustralian application number 2004201774, filed Apr. 28, 2004.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Apr. 30, 2018, isnamed 500028US03_SL.txt and is 643,248 bytes in size.

BACKGROUND

The invention relates to epitopes useful in the diagnosis and therapy ofcoeliac disease, including diagnostics, therapeutics, kits, and methodsof using the foregoing.

Coeliac disease is caused by an immune mediated hypersensitivity todietary gluten. Gluten proteins in wheat, rye, barley and in some casesoats are toxic in coeliac disease. Gluten is composed of alpha/beta,gamma and omega gliadins, and low and high molecular weight (LMW andHMW) glutenins in wheat, hordeins in barley, secalins in rye and aveninsin oats. Hordeins and secalins are homologous to gamma and omegagliadins and low and high molecular weight glutenins in wheat. Aveninsare phylogenetically more distant than hordeins and secalins from wheatgluten.

The goal of research in coeliac disease has been to define the toxiccomponents of gluten by defining the peptides that stimulategluten-specific T-cells. Precise definition of gluten epitopes permitsdevelopment of new diagnostics, therapeutics, tests for glutencontamination in food and non-toxic grains that retain thecooking/baking qualities of traditional gluten. Many of theseapplications require a comprehensive understanding of all rather thanthe most common toxic peptides in gluten.

Genes encoding HLA-DQ2 and/or HLA-DQ8 are present in over 99% ofindividuals with coeliac disease compared to approximately 35% of thegeneral Caucasian population. Gluten-derived peptides (epitopes) boundto HLA-DQ2 or HLA-DQ8 stimulate specific T-cells. HLA-DQ2 andDQ8-restricted epitopes include a “core” 9 amino acid sequence thatdirectly interacts with the peptide binding groove of HLA-DQ2 or DQ8 andwith cognate T-cell receptors. In general, libraries of overlappingpeptides (usually 15 to 20mers) containing all unique 10 or 12merpeptides in an antigen have been used to map HLA class II-restrictedT-cells epitopes.

A series of gluten peptides are known to activate gluten specificT-cells in coeliac disease. Previous studies have identified glutenpeptides from selected gluten proteins or gluten digests. T-cell clonesand lines isolated from intestinal biopsies have been used to screenthese gluten components.

Modification of gluten by the enzyme, tissue transglutaminase (tTG)present in intestinal tissue, substantially increases gluten'sstimulatory capacity on gluten specific T-cells. Most of the knownepitopes for gluten-specific T-cells correspond to tTG-deamidated glutenpeptides. Transglutaminase mediates deamidation of specific glutamineresidues (to glutamate) in gluten. Glutamine-containing sequencessusceptible to deamidation by tTG generally conform to a motif: QXPX(SEQ ID NO: 1929) or QXX (FYMILVW) (SEQ ID NO: 1942) (see Vader W. et al2002 J. Exp. Med. 195:643-649, PCT WO 03/066079, and Fleckenstein B.2002. J Biol Chem 277:34109-16). The motif for peptides that bind toHLA-DQ2 and that are susceptible to deamidation by tTG has been used topredict certain gluten epitopes (Vader et al J Exp Med 2002 J. Exp. Med.195:643-649, PCT WO 03/066079).

However, other groups have identified epitopes for gluten-specificintestinal T-cell clones and lines using panels of eleven recombinantalpha/beta (11) and five gamma gliadins (Arentz-Hansen H. 2000. J. Exp.Med. 191:603-612, Arentz-Hansen H. 2002. Gastroenterology 123:803-809,PCT WO 02/083722), and lysates of purified gluten proteins (Sjostrom H.et al 1998. Scand. J. Immunol. 48,111-115; van de Wal, Y. et al 1998. J.Immunol. 161(4):1585-1588; van de Wal, Y. et al 1999. Eur. J. Immunol.29:3133-3139; Vader W. et al 2002. Gastroenterology 122:1729-1737.).

Our work has exploited the observation that gluten challenge in vivoinduces HLA-DQ2 restricted CD4+ gluten-specific T-cells in peripheralblood expressing a gut-homing integrin (alpha4beta7). This techniqueallowed the mapping of the dominant epitope in A-gliadin (57-73 QE65)(Anderson, R P et al 2000. Nat. Med. 6:337-342., WO 01/25793). A-gliadin57-73 QE65 corresponds to two overlapping epitopes identified usingintestinal T-cell clones (Arentz-Hansen H. et al 2000. J. Exp. Med.191:603-612, Arentz-Hansen H. et al 2002. Gastroenterology 123:803-809).The advantage of in vivo gluten challenge to induce gluten specificT-cells is that any food can be consumed and the resulting T-cellsinduced in blood (quantified in peripheral blood using a simpleovernight interferon gamma ELISPOT assay) will have been stimulated invivo by endogenously presented epitopes, rather than primed in vitro bya synthetic or purified antigen. Overnight assays of fresh polyclonalperipheral blood T-cells also avoid the potential for artefactsassociated with the lengthy purification of T-cell clones.

Interestingly, T-cell clones and lines specific for severalgamma-gliadin epitopes (Arentz-Hansen H. 2002. Gastroenterology123:803-809, PCT WO 02/083722) cross-react with the originally definedA-gliadin epitope 57-73 QE65.

Although there is substantial homology within the alpha/beta gliadins,earlier work (see WO 03/104273) has shown that the dominant epitoperecognized in HLA-DQ2-associated coeliac disease, “A-gliadin 57-73QE65”, is encoded by a minority of the alpha/beta gliadins present inGenbank.

SUMMARY OF THE INVENTION

The current study set out to develop a method that would allow mappingof all T-cell epitopes in gluten. Consumption of wheat bread (200 gdaily for 3 days) or oats (100 g daily for 3 days) was used to inducegluten or avenin-specific T-cells in peripheral blood (collected 6 daysafter beginning the challenge). Peripheral blood mononuclear cells(PBMC) were assessed in overnight interferon gamma ELISPOT assays usinga library of gluten and avenin peptides including all unique 12mersequences included in every Genbank entry for wheat gluten and/or oatavenins. This goal was achieved by establishing an algorithm to designpeptides spanning all potential epitopes in gluten proteins in Genbank(2922 20mers included all 14 964 unique 9mers—potential T-cellepitopes), adapting the interferon-gamma ELISPOT assay to a highthroughput assay capable of screening over 1000 peptides with a singleindividual's blood and developing bioinformatics tools to analyse andinterpret the data generated.

A series of 41 “superfamilies” of wheat gluten peptides were identifiedas putative T-cell epitopes. Superfamilies shared motifs in which alimited level of redundancy was allowed. Many of the most potentfamilies include known T-cell epitopes including the previouslydescribed dominant epitope, A-gliadin 57-73.

Through comprehensive mapping of gluten epitopes using PBMC after glutenchallenge, the inventors have found a series of novel gliadin, LMW andHMW glutenin, and avenin epitopes for coeliac disease associated withHLA-DQ2 and HLA-DQ8. Novel epitopes were identified for HLA-DQ2 andHLA-DQ8-associated coeliac disease. HLA-DQ2 and HLA-DQ8 associatedcoeliac disease are genetically and functionally distinct in terms ofthe range of T-cell epitopes that are recognized. In addition, threepeptides present in avenin proteins of oats also activated peripheralblood mononuclear cells (PBMC) following oats challenge in HLA-DQ2+coeliac subjects, the first time oats epitopes have been defined.Identification of avenin peptides recognized by T-cells following oatschallenge in vivo provides a molecular basis for the observed occasionalrelapse of coeliacs following oat exposure (Lundin KEA et al. 2003 Gut52:1649-52) and may provide a basis for a predictive diagnostic orgenetic de-toxification of oats.

The data presented here will provide a comprehensive basis fordefinition of both common “dominant” and occasional “weak” T-cellepitopes in coeliac disease. This information is the platform forfunctional applications such as diagnostics, food tests,immunotherapeutics and prophylactics, and for design of non-toxic glutenproteins useful in modified grains.

In particular, through comprehensive mapping of gluten T cell epitopes,the inventors have found epitopes bioactive in coeliac disease inHLA-DQ2+ patients in wheat gliadins and glutenins, having similar coresequences (e.g., SEQ ID NOS: 1-199) and similar extended sequences(e.g., SEQ ID NOS:200-1554, 1555-1655, 1656-1671, and 1830-1903). Theinventors have also found epitopes bioactive in coeliac disease inHLA-DQ2+ patients in: oat avenins having similar core sequences (e.g.,SEQ ID NOS: 1684-1695) and similar extended sequences (e.g., SEQ ID NO:1672-1683, 1696-1698, and 1764-1768); rye secalins (SEQ ID NOS:1769-1786); and barley hordeins (SEQ ID NOS: 1787-1829). Additionally,epitopes bioactive in coeliac disease in HLA-DQ8+ patients have beenidentified in wheat gliadins having similar core sequences (e.g., SEQ IDNOS: 1699-1721) and similar extended sequences (e.g., SEQ ID NOS:1722-1763 and 1908-1927). This comprehensive mapping thus providesdominant epitopes recognized by T cells in coeliac patients. Thus, themethods of the invention described herein may be performed using any ofthese identified epitopes, and analogues and equivalents thereof. Thatis, the agents of the invention include these epitopes. Additionally,combinations of epitopes, i.e., “combitopes” or single peptidescomprising two or more epitiopes, have been shown to induce equivalentresponses as the individual epitopes, indicating that several epitopesmay be utilized for therapeutic, diagnostic, and other uses of theinvention. Such combitopes may be in the form of, e.g., SEQ ID NO: 1906.Preferably, the agents of the invention include one or more of theepitopes having the sequences listed recited in SEQ ID NOS: 1578-1579,1582-1583, 1587-1593, 1600-1620, 1623-1655, 1656-1671, 1672-1698,1699-1763, 1764-1768, 1769-1786, 1787-1829, 1895-1903, 1906, and1908-1927 and analogues and equivalents thereof as defined herein.

Preferred agents that are bioactive in coeliac disease in HLA-DQ8+patients possess a glutamine in a sequence that suggests susceptibilityto deamidation separated by seven residues from a second glutamine alsosusceptible to deamidation (e.g., as found in QGSFQPSQQ (SEQ ID NO:1710)) wherein the deamidated sequences are high affinity binders forHLA-DQ8 following deamidation by tTG (The binding motif for HLA-DQ8favours glutamate at positions 1 and 9.) In a less preferred embodiment,the agent possesses glutamine residues susceptible to deamidation butnot separated by seven residues from a second glutamine susceptible totTG-mediated deamidation.

The invention thus provides a method of diagnosing coeliac disease, orsusceptibility to coeliac disease, in an individual, comprising thesteps of: (a) contacting a sample from the host with an agent selectedfrom (i) the epitope comprising an amino acid sequence selected from SEQID NOS: 1-1927, preferably selected from SEQ ID NOS: 1578-1579,1582-1583, 1587-1593, 1600-1620, 1623-1655, 1656-1671, 1672-1698,1699-1763, 1764-1768, 1769-1786, 1787-1829, 1895-1903, 1906, and1908-1927, or an equivalent sequence from a naturally occurring glutenprotein, (ii) an analogue of (i) which is capable of being recognised bya T cell receptor that recognises (i), which in the case of a peptideanalogue is not more than 50 amino acids in length, or (iii) a productcomprising two or more agents as defined in (i) or (ii); and (b)determining in vitro whether T cells in the sample recognise the agent,with recognition by the T cells indicating that the individual has, oris susceptible to, coeliac disease.

The term “gluten protein” encompasses alpha/beta, gamma and omegagliadins, and low and high molecular weight (LMW and HMW) glutenins inwheat, hordeins in barley, secalins in rye, and avenins in oats. Theinvention is particularly concerned with gliadins and avenins.

The invention also provides use of the agent for the preparation of adiagnostic means for use in a method of diagnosing coeliac disease, orsusceptibility to coeliac disease, in an individual, said methodcomprising determining whether T cells of the individual recognise theagent, recognition by the T cells indicating that the individual has, oris susceptible to, coeliac disease.

The finding of epitopes which are modified by transglutaminase alsoallows diagnosis of coeliac disease based on determining whether othertypes of immune response to these epitopes are present. Thus theinvention also provides a method of diagnosing coeliac disease, orsusceptibility to coeliac disease, in an individual comprisingdetermining the presence of an antibody that binds to the epitope in asample from the individual, the presence of the antibody indicating thatthe individual has, or is susceptible to, coeliac disease.

The invention provides a method of determining whether a composition iscapable of causing coeliac disease comprising determining whether aprotein capable of being modified by a transglutaminase to anoligopeptide sequence as defined above is present in the composition,the presence of the protein indicating that the composition is capableof causing coeliac disease.

The invention also provides a mutant gluten protein whose wild-typesequence can be modified by a transglutaminase to a sequence thatcomprises an epitope comprising sequence as defined above, but whichmutant gluten protein has been modified in such a way that it does notcontain sequence which can be modified by a transglutaminase to asequence that comprises such an epitope comprising sequence; or afragment of such a mutant gluten protein which is at least 7 amino acidslong (e.g., at least 7, 8, 9, 10, 11, 12, 13, 14 or 15 amino acids long)and which comprises sequence which has been modified in said way.

The invention also provides a protein that comprises a sequence which isable to bind to a T cell receptor, which T cell receptor recognises theagent, and which sequence is able to cause antagonism of a T cell thatcarries such a T cell receptor.

Additionally the invention provides a food that comprises the proteinsdefined above.

The invention additionally provides the agent, optionally in associationwith a carrier, for use in a method of treating or preventing coeliacdisease by tolerising T cells which recognise the agent. Also providedis an antagonist of a T cell which has a T cell receptor that recognises(i), optionally in association with a carrier, for use in a method oftreating or preventing coeliac disease by antagonising such T cells.Additionally provided is the agent or an analogue that binds an antibody(that binds the agent) for use in a method of treating or preventingcoeliac disease in an individual by tolerising the individual to preventthe production of such an antibody.

The invention also provides methods of preventing or treating coeliacdisease comprising administering to an individual at least one agentselected from: a) a peptide comprising at least one epitope comprising asequence selected from the group consisting of SEQ ID NOs: 1-1927,preferably from the group consisting of SEQ ID NOS: 1578-1579,1582-1583, 1587-1593, 1600-1620, 1623-1655, 1656-1671, 1672-1698,1699-1763, 1764-1768, 1769-1786, 1787-1829, 1895-1903, 1906, and1908-1927, and equivalents thereof; and b) an analogue of a) which iscapable of being recognised by a T cell receptor that recognises thepeptide of a) and which is not more than 50 amino acids in length. Insome embodiments, the agent is HLA-DQ2-restricted, HLA-DQ8-restricted orone agent is HLA-DQ2-restricted and a second agent isHLA-DQ8-restricted. In some embodiments, the agent comprises a wheatepitope, an oat epitope, a rye epitope, a barley epitope or anycombination thereof either as a single agent or as multiple agents.

The present invention also provides methods of preventing or treatingcoeliac disease comprising administering to an individual apharmaceutical composition comprising an agent as described above andpharmaceutically acceptable carrier or diluent.

The present invention also provides methods of preventing or treatingcoeliac disease comprising administering to an individual apharmaceutical composition comprising an antagonist of a T cell whichhas a T cell receptor as defined above, and a pharmaceuticallyacceptable carrier or diluent.

The present invention also provides methods of preventing or treatingcoeliac disease comprising administering to an individual a compositionfor tolerising an individual to a gluten protein to suppress theproduction of a T cell or antibody response to an agent as definedabove, which composition comprises an agent as defined above.

The present invention also provides methods of preventing or treatingcoeliac disease by 1) diagnosing coeliac disease in an individual byeither: a) contacting a sample from the host with at least one agentselected from: i) a peptide comprising at least one epitope comprising asequence selected from the group consisting of: SEQ ID NOS: 1-1927,preferably selected from the group consisting of SEQ ID NOS: 1578-1579,1582-1583, 1587-1593, 1600-1620, 1623-1655, 1656-1671, 1672-1698,1699-1763, 1764-1768, 1769-1786, 1787-1829, 1895-1903, 1906, and1908-1927, and equivalents thereof; and ii) an analogue of i) which iscapable of being recognised by a T cell receptor that recognises i) andwhich is not more than 50 amino acids in length; and determining invitro whether T cells in the sample recognise the agent; recognition bythe T cells indicating that the individual has, or is susceptible to,coeliac disease; or b) administering an agent as defined above anddetermining in vivo whether T cells in the individual recognise theagent, recognition of the agent indicating that the individual has or issusceptible to coeliac disease; and 2) administering to an individualdiagnosed as having, or being susceptible to, coeliac disease atherapeutic agent for preventing or treating coeliac disease.

The present invention also provides agents as defined above, optionallyin association with a carrier, for use in a method of treating orpreventing coeliac disease by tolerising T cells which recognise theagent.

The present invention also provides antagonists of a T cell which has aT cell receptor as defined above, optionally in association with acarrier, for use in a method of treating or preventing coeliac diseaseby antagonising such T cells.

The present invention also provides proteins that comprises a sequencewhich is able to bind to a T cell receptor, which T cell receptorrecognises an agent as defined above, and which sequence is able tocause antagonism of a T cell that carries such a T cell receptor.

The present invention also provides pharmaceutical compositionscomprising an agent or antagonist as defined and a pharmaceuticallyacceptable carrier or diluent.

The present invention also provides compositions for tolerising anindividual to a gluten protein to suppress the production of a T cell orantibody response to an agent as defined above, which compositioncomprises an agent as defined above.

The present invention also provides compositions for antagonising a Tcell response to an agent as defined above, which composition comprisesan antagonist as defined above.

The present invention also provides mutant gluten proteins whosewild-type sequence can be modified by a transglutaminase to a sequencewhich is an agent as defined above, which mutant gluten proteincomprises a mutation which prevents its modification by atransglutaminase to a sequence which is an agent as defined above; or afragment of such a mutant gluten protein which is at least 7 amino acidslong (e.g., at least 7, 8, 9, 10, 11, 12, 13, 14 or 15 amino acids long)and which comprises the mutation.

The present invention also provides polynucleotides that comprise acoding sequence that encodes a protein or fragment as defined above.

The present invention also provides cells comprising a polynucleotide asdefined above or which have been transformed with such a polynucleotide.

The present invention also provides mammals that expresses a T cellreceptor as defined above.

The present invention also provides methods of diagnosing coeliacdisease, or susceptibility to coeliac disease, in an individualcomprising: a) contacting a sample from the host with at least one agentselected from i) a peptide comprising at least one epitope comprising asequence selected from the group consisting of: SEQ ID NOS: 1-1927,preferably selected from the group consisting of SEQ ID NOS: SEQ ID NOS:1578-1579, 1582-1583, 1587-1593, 1600-1620, 1623-1655, 1656-1671,1672-1698, 1699-1763, 1764-1768, 1769-1786, 1787-1829, 1895-1903, 1906,and 1908-1927, and equivalents thereof; and ii) an analogue of i) whichis capable of being recognised by a T cell receptor that recognises i)and which is not more than 50 amino acids in length; and b) determiningin vitro whether T cells in the sample recognise the agent; recognitionby the T cells indicating that the individual has, or is susceptible to,coeliac disease.

The present invention also provides methods of determining whether acomposition is capable of causing coeliac disease comprising determiningwhether a protein capable of being modified by a transglutaminase to anoligopeptide sequence is present in the composition, the presence of theprotein indicating that the composition is capable of causing coeliacdisease.

The present invention also provides methods of identifying an antagonistof a T cell, which T cell recognises an agent as defined above,comprising contacting a candidate substance with the T cell anddetecting whether the substance causes a decrease in the ability of theT cell to undergo an antigen specific response, the detecting of anysuch decrease in said ability indicating that the substance is anantagonist.

The present invention also provides kits for carrying out any of themethods described above comprising an agent as defined above and a meansto detect the recognition of the peptide by the T cell.

The present invention also provides methods of identifying a productwhich is therapeutic for coeliac disease comprising administering acandidate substance to a mammal as defined above which has, or which issusceptible to, coeliac disease and determining whether substanceprevents or treats coeliac disease in the mammal, the prevention ortreatment of coeliac disease indicating that the substance is atherapeutic product.

The present invention also provides processes for the production of aprotein encoded by a coding sequence as defined above which processcomprises: a) cultivating a cell described above under conditions thatallow the expression of the protein; and optionally b) recovering theexpressed protein.

The present invention also provides methods of obtaining a transgenicplant cell comprising transforming a plant cell with a vector asdescribed above to give a transgenic plant cell.

The present invention also provides methods of obtaining afirst-generation transgenic plant comprising regenerating a transgenicplant cell transformed with a vector as described above to give atransgenic plant.

The present invention also provides methods of obtaining a transgenicplant seed comprising obtaining a transgenic seed from a transgenicplant obtainable as described above.

The present invention also provides methods of obtaining a transgenicprogeny plant comprising obtaining a second-generation transgenicprogeny plant from a first-generation transgenic plant obtainable by amethod as described above, and optionally obtaining transgenic plants ofone or more further generations from the second-generation progeny plantthus obtained.

The present invention also provides transgenic plant cells, plants,plant seeds or progeny plants obtainable by any of the methods describedabove.

The present invention also provides transgenic plants or plant seedscomprising plant cells as described above.

The present invention also provides transgenic plant cell callusescomprising plant cells as described above obtainable from a transgenicplant cell, first-generation plant, plant seed or progeny as definedabove.

The present invention also provides methods of obtaining a crop productcomprising harvesting a crop product from a plant according to anymethod described above and optionally further processing the harvestedproduct.

The present invention also provides food that comprises a protein asdefined above.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a method to generate all possible peptide epitopes from agroup of proteins.

FIG. 2A and FIG. 2B show Genbank accession numbers for gluten geneproducts present in the Genbank database on 16 Jun. 2003 (see FIG. 2Aand FIG. 2B).

FIG. 3A shows an expectation maximization (EM) algorithm to analyze datafrom ELISpot.

FIG. 3B shows a test on a dataset of patients with coeliac disease.

FIG. 4 shows an iterative procedure to find minimal set of responsiveepitopes.

FIG. 5A, FIG. 5B, FIG. 5C, FIG. 5D, FIG. 5E, FIG. 5F, FIG. 5G, FIG. 5H,FIG. 5I, FIG. 5J, FIG. 5K, FIG. 5L, FIG. 5M, FIG. 5N, FIG. 5O, FIG. 5P,FIG. 5Q, FIG. 5R, FIG. 5S, FIG. 5T, FIG. 5U, FIG. 5W, FIG. 5V, FIG. 5X,FIG. 5Y, FIG. 5Z, and FIG. 5AA show gliadin and glutenin sequences (SEQID NOS: 1-1554). In the “consensus” column, letters in lower case usethe standard one letter amino acid code, but letters in upper case havea different meaning: E=[e or q], F=[f or y or w], I=[i or l or v], S=[sor t], R=[r or k or h]. The “sequence” column uses the standard oneletter amino acid code.

FIG. 6A, FIG. 6B, FIG. 6C, and FIG. 6D show gluten peptides thatstimulate gamma interferon in PBMC collected 6 days after glutenchallenge in HLA-DQ2+ coeliac disease volunteers (SEQ ID NOS:1555-1655). The indicated 9mers are common to 200 groups of bioactive“structurally” related 20mer peptides. The gluten sequences are rankedaccording to the bioactivity×proportion of subjects responding.

FIG. 7 shows the results of a wheat challenge experiment (SEQ ID NOS:1656-1671). These peptides gave high quality responses (indicated ‘Y’)in ten subjects (A-J) after wheat challenge.

FIG. 8 shows Avenin peptides (+/−deamidation by tTG) that stimulateinterferon-γ in PBMC collected 6 days after gluten challenge in HLA-DQ2+coeliac disease volunteers (SEQ ID NOS: 1672-1698). Those marked witha * are optimal unique 20mers inducing IFN-γ after oats challenge.

FIG. 9 shows the most potent 40 20mers (SEQ ID NOS: 1699-1763) in twoHLA-DQ8 (not HLA-DQ2) subjects grouped according to shared coresequences. The core sequence of group 6 (QGSFQPSQQ (SEQ ID NO: 1710))corresponds to the alpha-gliadin epitope described by van de Wal et al(J. Immunol. 1998, 161(4):1585-1588). The maximum response in Subject Awas 271 SFC (medium alone, no peptide response: 4 SFC), and in B it was26 SFC (medium alone, no peptide response: 1 SFC).

FIG. 10 shows the amino acid sequence of A-gliadin (SEQ ID NO: 1928)based on amino acid sequencing.

DETAILED DESCRIPTION OF THE INVENTION

The term “coeliac disease” encompasses a spectrum of conditions causedby varying degrees of gluten sensitivity, including a severe formcharacterised by a flat small intestinal mucosa (hyperplastic villousatrophy) and other forms characterised by milder symptoms.

The individual mentioned above (in the context of diagnosis or therapy)is human. They may have coeliac disease (symptomatic or asymptomatic) orbe suspected of having it. They may be on a gluten free diet. They maybe in an acute phase response (for example they may have coeliacdisease, but have only ingested gluten in the last 24 hours before whichthey had been on a gluten free diet for 14 to 28 days).

The individual may be susceptible to coeliac disease, such as a geneticsusceptibility (determined for example by the individual havingrelatives with coeliac disease or possessing genes which causepredisposition to coeliac disease).

The Agent

The agent is typically a peptide, for example of length 7 to 50 aminoacids, such as 10 to 40, 12 to 35 or 15 to 30 amino acids in length.

The agent may be the peptide represented by any of SEQ ID NOS: 1-1927 oran epitope comprising sequence that comprises any of SEQ ID NOS: 1-1927which is an isolated oligopeptide derived from a gluten protein; or anequivalent of these sequences from a naturally occurring gluten protein.In a further set of embodiments of the invention, the agent is anypeptide epitope of an oat gluten (e.g. any T cell epitope of an avenin).

Preferably, the agent is the peptide represented by any of SEQ ID NOS:1578-1579, 1582-1583, 1587-1593, 1600-1620, 1623-1655, 1656-1671,1672-1698, 1699-1763, 1764-1768, 1769-1786, 1787-1829, 1895-1903, 1906,and 1908-1927 or an epitope comprising sequence that comprises any ofSEQ ID NOS: 1578-1579, 1582-1583, 1587-1593, 1600-1620, 1623-1655,1656-1671, 1672-1698, 1699-1763, 1764-1768, 1769-1786, 1787-1829,1895-1903, 1906, and 1908-1927 which is an isolated oligopeptide derivedfrom a gluten protein; or an equivalent of these sequences from anaturally occurring gluten protein.

Thus the epitope may be a derivative of a naturally occurring glutenprotein, particularly from a wheat or oat gluten. Such a derivative istypically a fragment of the gluten protein, or a mutated derivative ofthe whole protein or fragment. Therefore the epitope of the inventiondoes not include the naturally occurring whole gluten protein, and doesnot include other whole naturally occurring gluten proteins.

Typically such fragments will be at least 7 amino acids in length (e.g.,at least 7, 8, 9, 10, 11, 12, 13, 14 or 15 amino acids in length).

Typically such fragments will be recognised by T cells to at least thesame extent that the agents from which they are derived are recognisedin any of the assays described herein using samples from coeliac diseasepatients.

The agent may be the peptide represented by any of SEQ ID NOS: 1-1927,preferably the peptide represented by any of SEQ ID NOS: 1578-1579,1582-1583, 1587-1593, 1600-1620, 1623-1655, 1656-1671, 1672-1698,1699-1763, 1764-1768, 1769-1786, 1787-1829, 1895-1903, 1906, and1908-1927 or a protein comprising a sequence corresponding to any of SEQID NOS: 1-1927, preferably comprising a sequence corresponding to any offrom SEQ ID NOS: 1578-1579, 1582-1583, 1587-1593, 1600-1620, 1623-1655,1656-1671, 1672-1698, 1699-1763, 1764-1768, 1769-1786, 1787-1829,1895-1903, 1906, and 1908-1927 (such as fragments of a gluten proteincomprising any of SEQ ID NOS: 1-1927 and preferably any of from SEQ IDNOS: 1578-1579, 1582-1583, 1587-1593, 1600-1620, 1623-1655, 1656-1671,1672-1698, 1699-1763, 1764-1768, 1769-1786, 1787-1829, 1895-1903, 1906,and 1908-1927, for example after the gluten protein has been treatedwith transglutaminase). Bioactive fragments of such sequences are alsoagents of the invention. Typically such fragments will be at least 7amino acids in length (e.g., at least 7, 8, 9, 10, 11, 12, 13, 14 or 15amino acids in length). Sequences equivalent to any of SEQ ID NOS:1-1927 or analogues of these sequences are also agents of the invention.

In the case where the epitope comprises a sequence equivalent to theabove epitopes (including fragments) from another gluten protein (e.g.any of the gluten proteins mentioned herein or any gluten proteins whichcause coeliac disease), such equivalent sequences will correspond to afragment of a gluten protein typically treated (partially or fully) withtransglutaminase. Such equivalent peptides can be determined by aligningthe sequences of other gluten proteins with the gluten protein fromwhich the original epitope derives (for example using any of theprograms mentioned herein). Transglutaminase is commercially available(e.g. Sigma T-5398).

The agent which is an analogue is capable of being recognised by a TCRwhich recognises (i). Therefore generally when the analogue is added toT cells in the presence of (i), typically also in the presence of anantigen presenting cell (APC) (such as any of the APCs mentionedherein), the analogue inhibits the recognition of (i), i.e. the analogueis able to compete with (i) in such a system.

The analogue may be one which is capable of binding the TCR whichrecognises (i). Such binding can be tested by standard techniques. SuchTCRs can be isolated from T cells which have been shown to recognise (i)(e.g. using the method of the invention). Demonstration of the bindingof the analogue to the TCRs can then shown by determining whether theTCRs inhibit the binding of the analogue to a substance that binds theanalogue, e.g. an antibody to the analogue. Typically the analogue isbound to a class II MHC molecule (e.g. HLA-DQ2) in such an inhibition ofbinding assay.

Typically the analogue inhibits the binding of (i) to a TCR. In thiscase the amount of (i) which can bind the TCR in the presence of theanalogue is decreased. This is because the analogue is able to bind theTCR and therefore competes with (i) for binding to the TCR.

T cells for use in the above binding experiments can be isolated frompatients with coeliac disease, for example with the aid of the method ofthe invention. Other binding characteristics of the analogue may also bethe same as (i), and thus typically the analogue binds to the same MHCclass II molecule to which the peptide binds (HLA-DQ2 or -DQ8). Theanalogue typically binds to antibodies specific for (i), and thusinhibits binding of (i) to such antibodies.

The analogue is typically a peptide. It may have homology with (i),typically at least 70% homology, preferably at least 80, 90%, 95%, 97%or 99% homology with (i), for example over a region of at least 7, 8, 9,10, 11, 12, 13, 14, 15 or more (such as the entire length of theanalogue and/or (i), or across the region which contacts the TCR orbinds the MHC molecule) contiguous amino acids. Methods of measuringprotein homology are well known in the art and it will be understood bythose of skill in the art that in the present context, homology iscalculated on the basis of amino acid identity (sometimes referred to as“hard homology”).

For example the UWGCG Package provides the BESTFIT program which can beused to calculate homology (for example used on its default settings)(Devereux et al (1984) Nucleic Acids Research 12, p387-395). The PILEUPand BLAST algorithms can be used to calculate homology or alignsequences (typically on their default settings), for example asdescribed in Altschul S. F. (1993) J Mol Evol 36:290-300; Altschul, S, Fet al (1990) J Mol Biol 215:403-10.

Software for performing BLAST analyses is publicly available through theNational Center for Biotechnology Information on the world wide webthrough the Internet at, for example, “www.ncbi.nlm.nih.gov/”. Thisalgorithm involves first identifying high scoring sequence pair (HSPs)by identifying short words of length W in the query sequence that eithermatch or satisfy some positive-valued threshold score T when alignedwith a word of the same length in a database sequence. T is referred toas the neighbourhood word score threshold (Altschul et al, supra). Theseinitial neighbourhood word hits act as seeds for initiating searches tofind HSPs containing them. The word hits are extended in both directionsalong each sequence for as far as the cumulative alignment score can beincreased. Extensions for the word hits in each direction are haltedwhen: the cumulative alignment score falls off by the quantity X fromits maximum achieved value; the cumulative score goes to zero or below,due to the accumulation of one or more negative-scoring residuealignments; or the end of either sequence is reached. The BLASTalgorithm parameters W, T and X determine the sensitivity and speed ofthe alignment. The BLAST program uses as defaults a word length (W) of11, the BLOSUM62 scoring matrix (see Henikoff and Henikoff (1992) Proc.Natl. Acad. Sci. USA 89: 10915-10919) alignments (B) of 50, expectation(E) of 10, M=5, N=4, and a comparison of both strands.

The BLAST algorithm performs a statistical analysis of the similaritybetween two sequences; see e.g., Karlin and Altschul (1993) Proc. Natl.Acad. Sci. USA 90: 5873-5787. One measure of similarity provided by theBLAST algorithm is the smallest sum probability (P(N)), which providesan indication of the probability by which a match between two nucleotideor amino acid sequences would occur by chance. For example, a sequenceis considered similar to another sequence if the smallest sumprobability in comparison of the first sequence to the second sequenceis less than about 1, preferably less than about 0.1, more preferablyless than about 0.01, and most preferably less than about 0.001.

The homologous peptide analogues typically differ from (i) by 1, 2, 3,4, 5, 6, 7, 8 or more mutations (which may be substitutions, deletionsor insertions). These mutations may be measured across any of theregions mentioned above in relation to calculating homology. Thesubstitutions are preferably ‘conservative’. These are defined accordingto the following Table.

Amino acids in the same block in the second column and preferably in thesame line in the third column may be substituted for each other:

ALIPHATIC Non-polar G A P I L V Polar-uncharged C S T M N QPolar-charged D E K R AROMATIC H F W Y

Typically the amino acids in the analogue at the equivalent positions toamino acids in (i) that contribute to binding the MHC molecule or areresponsible for the recognition by the TCR, are the same or areconserved.

Typically the analogue peptide comprises one or more modifications,which may be natural post-translation modifications or artificialmodifications. The modification may provide a chemical moiety (typicallyby substitution of a hydrogen, e.g. of a C—H bond), such as an amino,acetyl, hydroxy or halogen (e.g. fluorine) group or carbohydrate group.Typically the modification is present on the N or C terminus.

The analogue may comprise one or more non-natural amino acids, forexample amino acids with a side chain different from natural aminoacids. Generally, the non-natural amino acid will have an N terminusand/or a C terminus. The non-natural amino acid may be an L- or aD-amino acid.

The analogue typically has a shape, size, flexibility or electronicconfiguration that is substantially similar to (i). It is typically aderivative of (i). In one embodiment the analogue is a fusion proteincomprising the sequence of any of SEQ ID NOS: 1-1927 and non-glutensequence. Preferably, the analogue according to this embodiment is afusion protein comprising the sequence of any of SEQ ID NOs: 1578-1579,1582-1583, 1587-1593, 1600-1620, 1623-1655, 1656-1671, 1672-1698,1699-1763, 1764-1768, 1769-1786, 1787-1829, 1895-1903, 1906, and1908-1927 and non-gluten sequence

In one embodiment the analogue is or mimics (i) bound to a MHC class IImolecule. 2, 3, 4 or more of such complexes may be associated or boundto each other, for example using a biotin/streptavidin based system, inwhich typically 2, 3 or 4 biotin labelled MHC molecules bind to astreptavidin moiety. This analogue typically inhibits the binding of the(i)/MHC Class II complex to a TCR or antibody which is specific for thecomplex.

The analogue is typically an antibody or a fragment of an antibody, suchas a Fab or F(ab′)₂ fragment. The analogue may be immobilised on a solidsupport, particularly an analogue that mimics peptide bound to a MHCmolecule.

The analogue is typically designed by computational means and thensynthesised using methods known in the art. Alternatively the analoguecan be selected from a library of compounds. The library may be acombinatorial library or a display library, such as a phage displaylibrary. The library of compounds may be expressed in the displaylibrary in the form of being bound to a MHC class II molecule, such asHLA-DQ2 or -DQ8. Analogues are generally selected from the library basedon their ability to mimic the binding characteristics (i). Thus they maybe selected based on ability to bind a TCR or antibody which recognises(i).

Typically analogues will be recognised by T cells to at least the sameextent as any of the agents (i), for example at least to the same extentas the equivalent epitope is recognised in any of the assays describedherein, typically using T cells from coeliac disease patients. Analoguesmay be recognised to these extents in vivo and thus may be able toinduce coeliac disease symptoms to at least the same extent as any ofthe agents mentioned herein (e.g. in a human patient or animal model).

Analogues may be identified in a method comprising determining whether acandidate substance is recognised by a T cell receptor that recognisesan epitope of the invention, recognition of the substance indicatingthat the substance is an analogue. Such TCRs may be any of the TCRsmentioned herein, and may be present on T cells. Any suitable assaymentioned herein can be used to identify the analogue. In one embodimentthis method is carried out in vivo.

As mentioned above preferred analogues are recognised to at least thesame extent as the equivalent epitope, and so the method may be used toidentify analogues which are recognised to this extent.

In one embodiment the method comprises determining whether a candidatesubstance is able to inhibit the recognition of an epitope of theinvention, inhibition of recognition indicating that the substance is ananalogue.

The agent may be a product comprising at least 2, 5, 10 or 20 agents asdefined by (i) or (ii). Typically the composition comprises epitopes ofthe invention (or equivalent analogues) from different gluten proteins,such as any of the species or variety of or types of gluten proteinmentioned herein. Preferred compositions comprise at least one epitopeof the invention, or equivalent analogue, from all of the glutenspresent in any of the species or variety mentioned herein, or from 2, 3,4 or more of the species mentioned herein (such as from the panel ofspecies consisting of wheat, rye, barley, oats and triticale). Thus, theagent may be monovalent or multivalent.

According to certain embodiments of the invention, the agent does nothave or is not based on a sequence disclosed in WO 02/083722 and/or WO01/25793 and/or WO03/104273 and/or recited in any of SEQ ID NOS:1555-1577, 1580-1581, 1584-1586, 1594-1599, 1621-1622 and/or is not anagent derived from A-gliadin, the sequence of which is given in FIG. 10.

Within SEQ ID NOs: 1-1927, a preferred subset is SEQ ID NOs: 1-1763.Within SEQ ID NOs: 1764-1927, preferred subsets are: (a) oat sequences1764-1768, (b) rye sequences 1769-1786, (c) barley sequences 1787-1829,(d) wheat sequences 1895-1903, (e) wheat DQ8 sequences 1908-1927, and(f) combitope sequence 1906. Other preferred subsets are: (a) 1764-1768,(b) 1769-1773, (c) 1774-1786, (d) 1787-1792, (e) 1793-1829, (f)1830-1894, (g) 1895-1903, (h) 1830-1903, (i) 1904-1906, (j) 1908-1916,(k) 1917-1927, and (1) 1908-1913, 1915-1923 and 1925-1927.

Within SEQ ID NOs: 1578-1579, 1582-1583, 1587-1593, 1600-1620,1623-1655, 1656-1671, 1672-1698, 1699-1763, & 1764-1927, particularlypreferred wheat epitopes are SEQ ID NOs: 1656-1671, 1830-1903, and1907-1927.

Within SEQ ID NOs: 1830-1894 (Table 1), some sequences have N-terminaland C-terminal glycines. The invention extends to these sequencesomitting the C-terminal glycine and/or the N-terminal glycine.Preferably, both the C-terminal glycine and the N-terminal glycine areomitted.

Diagnosis

As mentioned above the method of diagnosis of the invention may be basedon the detection of T cells that bind the agent or on the detection ofantibodies that recognise the agent.

The T cells that recognise the agent in the method (which includes theuse mentioned above) are generally T cells that have been pre-sensitisedin vivo to one or more gluten proteins. As mentioned above suchantigen-experienced T cells have been found to be present in theperipheral blood.

In the method the T cells can be contacted with the agent in vitro or invivo, and determining whether the T cells recognise the agent can beperformed in vitro or in vivo. Thus the invention provides the agent foruse in a method of diagnosis practiced on the human body. Differentagents are provided for simultaneous, separate or sequential use in sucha method.

The in vitro method is typically carried out in aqueous solution intowhich the agent is added. The solution will also comprise the T cells(and in certain embodiments the APCs discussed below). The term‘contacting’ as used herein includes adding the particular substance tothe solution.

Determination of whether the T cells recognise the agent is generallyaccomplished by detecting a change in the state of the T cells in thepresence of the agent or determining whether the T cells bind the agent.The change in state is generally caused by antigen specific functionalactivity of the T cell after the TCR binds the agent. The change ofstate may be measured inside (e.g. change in intracellular expression ofproteins) or outside (e.g. detection of secreted substances) the Tcells.

The change in state of the T cell may be the start of or increase insecretion of a substance from the T cell, such as a cytokine, especiallyIFN-γ, IL-2 or TNF-α. Determination of IFN-γ secretion is particularlypreferred. The substance can typically be detected by allowing it tobind to a specific binding agent and then measuring the presence of thespecific binding agent/substance complex. The specific binding agent istypically an antibody, such as polyclonal or monoclonal antibodies.Antibodies to cytokines are commercially available, or can be made usingstandard techniques.

Typically the specific binding agent is immobilised on a solid support.After the substance is allowed to bind the solid support can optionallybe washed to remove material which is not specifically bound to theagent. The agent/substance complex may be detected by using a secondbinding agent that will bind the complex. Typically the second agentbinds the substance at a site which is different from the site whichbinds the first agent. The second agent is preferably an antibody and islabelled directly or indirectly by a detectable label.

Thus the second agent may be detected by a third agent that is typicallylabelled directly or indirectly by a detectable label. For example thesecond agent may comprise a biotin moiety, allowing detection by a thirdagent which comprises a streptavidin moiety and typically alkalinephosphatase as a detectable label.

In one embodiment the detection system which is used is the ex-vivoELISPOT assay described in WO 98/23960. In that assay IFN-γ secretedfrom the T cell is bound by a first IFN-γ specific antibody that isimmobilised on a solid support. The bound IFN-γ is then detected using asecond IFN-γ specific antibody which is labelled with a detectablelabel. Such a labelled antibody can be obtained from MABTECH (Stockholm,Sweden). Other detectable labels which can be used are discussed below.

The change in state of the T cell that can be measured may be theincrease in the uptake of substances by the T cell, such as the uptakeof thymidine. The change in state may be an increase in the size of theT cells, or proliferation of the T cells, or a change in cell surfacemarkers on the T cell.

In one embodiment the change of state is detected by measuring thechange in the intracellular expression of proteins, for example theincrease in intracellular expression of any of the cytokines mentionedabove. Such intracellular changes may be detected by contacting theinside of the T cell with a moiety that binds the expressed proteins ina specific manner and which allows sorting of the T cells by flowcytometry.

In one embodiment when binding the TCR the agent is bound to an MHCclass II molecule (typically HLA-DQ2 or -DQ8), which is typicallypresent on the surface of an antigen presenting cell (APC). However asmentioned herein other agents can bind a TCR without the need to alsobind an MHC molecule.

Generally the T cells which are contacted in the method are taken fromthe individual in a blood sample, although other types of samples whichcontain T cells can be used. The sample may be added directly to theassay or may be processed first. Typically the processing may comprisediluting of the sample, for example with water or buffer. Typically thesample is diluted from 1.5 to 100 fold, for example 2 to 50 or 5 to 10fold.

The processing may comprise separation of components of the sample.Typically mononuclear cells (MCs) are separated from the samples. TheMCs will comprise the T cells and APCs. Thus in the method the APCspresent in the separated MCs can present the peptide to the T cells. Inanother embodiment only T cells, such as only CD4 T cells, can bepurified from the sample. PBMCs, MCs and T cells can be separated fromthe sample using techniques known in the art, such as those described inLalvani et al (1997) J. Exp. Med. 186, p859-865.

In one embodiment, the T cells used in the assay are in the form ofunprocessed or diluted samples, or are freshly isolated T cells (such asin the form of freshly isolated MCs or PBMCs) which are used directly exvivo, i.e. they are not cultured before being used in the method. Thusthe T cells have not been restimulated in an antigen specific manner invitro. However the T cells can be cultured before use, for example inthe presence of one or more of the agents, and generally also exogenousgrowth promoting cytokines. During culturing the agent(s) are typicallypresent on the surface of APCs, such as the APC used in the method.Pre-culturing of the T cells may lead to an increase in the sensitivityof the method. Thus the T cells can be converted into cell lines, suchas short term cell lines (for example as described in Ota et al (1990)Nature 346, p183-187).

The APC that is typically present in the method may be from the sameindividual as the T cell or from a different host. The APC may be anaturally occurring APC or an artificial APC. The APC is a cell that iscapable of presenting the peptide to a T cell. It is typically a B cell,dendritic cell or macrophage. It is typically separated from the samesample as the T cell and is typically co-purified with the T cell. Thusthe APC may be present in MCs or PBMCs. The APC is typically a freshlyisolated ex vivo cell or a cultured cell. It may be in the form of acell line, such as a short term or immortalised cell line. The APC mayexpress empty MHC class II molecules on its surface.

In the method one or more (different) agents may be used. Typically theT cells derived from the sample can be placed into an assay with all theagents which it is intended to test or the T cells can be divided andplaced into separate assays each of which contain one or more of theagents.

The invention also provides the agents such as two or more of any of theagents mentioned herein (e.g. the combinations of agents which arepresent in the composition agent discussed above) for simultaneousseparate or sequential use (eg. for in vivo use).

In one embodiment agent per se is added directly to an assay comprisingT cells and APCs. As discussed above the T cells and APCs in such anassay could be in the form of MCs. When agents that can be recognised bythe T cell without the need for presentation by APCs are used then APCsare not required. Analogues which mimic the original (i) bound to a MHCmolecule are an example of such an agent.

In one embodiment the agent is provided to the APC in the absence of theT cell. The APC is then provided to the T cell, typically after beingallowed to present the agent on its surface. The peptide may have beentaken up inside the APC and presented, or simply be taken up onto thesurface without entering inside the APC.

The duration for which the agent is contacted with the T cells will varydepending on the method used for determining recognition of the peptide.Typically 10⁵ to 10⁷, preferably 5×10⁵ to 10⁶ PBMCs are added to eachassay. In the case where agent is added directly to the assay itsconcentration is from 10⁻¹ to 10³ μg/ml, preferably 0.5 to 50 μg/ml or 1to 10 μg/ml.

Typically the length of time for which the T cells are incubated withthe agent is from 4 to 24 hours, preferably 6 to 16 hours. When using exvivo PBMCs it has been found that 0.3×10⁶ PBMCs can be incubated in 10μg/ml of peptide for 12 hours at 37° C.

The determination of the recognition of the agent by the T cells may bedone by measuring the binding of the agent to the T cells (this can becarried out using any suitable binding assay format discussed herein).Typically T cells which bind the agent can be sorted based on thisbinding, for example using a FACS machine. The presence of T cells thatrecognise the agent will be deemed to occur if the frequency of cellssorted using the agent is above a “control” value. The frequency ofantigen-experienced T cells is generally 1 in 10⁶ to 1 in 10³, andtherefore whether or not the sorted cells are antigen-experienced Tcells can be determined.

The determination of the recognition of the agent by the T cells may bemeasured in vivo. Typically the agent is administered to the host andthen a response which indicates recognition of the agent may bemeasured. The agent is typically administered intradermally orepidermally. The agent is typically administered by contacting with theoutside of the skin, and may be retained at the site with the aid of aplaster or dressing. Alternatively the agent may be administered byneedle, such as by injection, but can also be administered by othermethods such as ballistics (e.g. the ballistics techniques which havebeen used to deliver nucleic acids). EP-A-0693119 describes techniquesthat can typically be used to administer the agent. Typically from 0.001to 1000 μg, for example from 0.01 to 100 μg or 0.1 to 10 μg of agent isadministered.

In one embodiment a product can be administered which is capable ofproviding the agent in vivo. Thus a polynucleotide capable of expressingthe agent can be administered, typically in any of the ways describedabove for the administration of the agent. The polynucleotide typicallyhas any of the characteristics of the polynucleotide provided by theinvention which is discussed below. The agent is expressed from thepolynucleotide in vivo. Typically from 0.001 to 1000 μg, for examplefrom 0.01 to 100 μg or 0.1 to 10 μg of polynucleotide is administered.

Recognition of the agent administered to the skin is typically indicatedby the occurrence of inflammation (e.g. induration, erythema or oedema)at the site of administration. This is generally measured by visualexamination of the site.

The method of diagnosis based on the detection of an antibody that bindsthe agent is typically carried out by contacting a sample from theindividual (such as any of the samples mentioned here, optionallyprocessed in any manner mentioned herein) with the agent and determiningwhether an antibody in the sample binds the agent, such a bindingindicating that the individual has, or is susceptible to coeliacdisease. Any suitable format of binding assay may be used, such as anysuch format mentioned herein.

Therapy

The identification of the immunodominant epitope and other epitopesdescribed herein allows therapeutic products to be made which target theT cells which recognise this epitope (such T cells being ones whichparticipate in the immune response against gluten proteins). Thesefindings also allow the prevention or treatment of coeliac disease bysuppressing (by tolerisation) an antibody or T cell response to theepitope(s).

Certain agents of the invention bind the TCR that recognises the epitopeof the invention (as measured using any of the binding assays discussedabove) and cause tolerisation of the T cell that carries the TCR. Suchagents, optionally in association with a carrier, can therefore be usedto prevent or treat coeliac disease.

Generally tolerisation can be caused by the same peptides which can(after being recognised by the TCR) cause antigen specific functionalactivity of the T cell (such as any such activity mentioned herein, e.g.secretion of cytokines). Such agents cause tolerisation when they arepresented to the immune system in a ‘tolerising’ context.

Tolerisation leads to a decrease in the recognition of a T cell orantibody epitope by the immune system. In the case of a T cell epitopethis can be caused by the deletion or anergising of

T cells that recognise the epitope. Thus T cell activity (for example asmeasured in suitable assays mentioned herein) in response to the epitopeis decreased. Tolerisation of an antibody response means that adecreased amount of specific antibody to the epitope is produced whenthe epitope is administered.

Methods of presenting antigens to the immune system in such a contextare known and are described for example in Yoshida et al. Clin. Immunol.Immunopathol. 82, 207-215 (1997), Thurau et al. Clin. Exp. Immunol. 109,370-6 (1997), and Weiner et al. Res. Immunol. 148, 528-33 (1997). Inparticular certain routes of administration can cause tolerisation, suchas oral, nasal or intraperitoneal. Tolerisation may also be accomplishedvia dendritic cells and tetramers presenting peptide. Particularproducts which cause tolerisation may be administered (e.g. in acomposition that also comprises the agent) to the individual. Suchproducts include cytokines, such as cytokines that favour a Th2 response(e.g. IL-4, TGF-β or IL-10). Products or agent may be administered at adose that causes tolerisation.

The invention provides a protein that comprises a sequence able to actas an antagonist of the T cell (which T cell recognises the agent). Suchproteins and such antagonists can also be used to prevent or treatcoeliac disease. The antagonist will cause a decrease in the T cellresponse. In one embodiment, the antagonist binds the TCR of the T cell(generally in the form of a complex with HLA-DQ2 or -DQ8) but instead ofcausing normal functional activation causing an abnormal signal to bepassed through the TCR intracellular signalling cascade, which causesthe T cell to have decreased function activity (e.g. in response torecognition of an epitope, typically as measured by any suitable assaymentioned herein).

In one embodiment the antagonist competes with epitope to bind acomponent of MHC processing and presentation pathway, such as an MHCmolecule (typically HLA-DQ2 or -DQ8). Thus the antagonist may bindHLA-DQ2 or -DQ8 (and thus be a peptide presented by this MHC molecule)or a homologue thereof.

Methods of causing antagonism are known in the art. In one embodimentthe antagonist is a homologue of the epitopes mentioned above and mayhave any of the sequence, binding or other properties of the agent(particularly analogues). The antagonists typically differ from any ofthe above epitopes (which are capable of causing a normal antigenspecific function in the T cell) by 1, 2, 3, 4 or more mutations (eachof which may be a substitution, insertion or deletion). Such antagonistsare termed “altered peptide ligands” or “APL” in the art. The mutationsare typically at the amino acid positions that contact the TCR.

For example, the antagonist may differ from the epitope by asubstitution within the sequence that is equivalent to the sequencerepresented by amino acids 64 to 67 of A-gliadin (the sequence ofA-gliadin is given in FIG. 10). Thus preferably the antagonist has asubstitution at the equivalent of position 64, 65 or 67. Preferably thesubstitution is 64W, 67W, 67M or 65T.

Since the T cell immune response to the epitope of the invention in anindividual is polyclonal, more than one antagonist may need to beadministered to cause antagonism of T cells of the response which havedifferent TCRs. Therefore the antagonists may be administered in acomposition which comprises at least 2, 4, 6 or more differentantagonists, which each antagonise different T cells.

The invention also provides a method of identifying an antagonist of a Tcell (which recognises the agent), comprising contacting a candidatesubstance with the T cell and detecting whether the substance causes adecrease in the ability of the T cell to undergo an antigen specificresponse (e.g. using any suitable assay mentioned herein), the detectingof any such decrease in said ability indicating that the substance is anantagonist.

In one embodiment, the antagonists (including combinations ofantagonists to a particular epitope) or tolerising (T cell and antibodytolerising) agents are present in a composition comprising at least 2,4, 6 or more antagonists or agents which antagonise or tolerise todifferent epitopes of the invention, for example to the combinations ofepitopes discussed above in relation to the agents which are a productcomprising more than one substance.

Testing Whether a Composition is Capable of Causing Coeliac Disease

As mentioned above the invention provides a method of determiningwhether a composition is capable of causing coeliac disease comprisingdetecting the presence of a protein sequence which is capable of beingmodified by a transglutaminase to as sequence comprising the agent orepitope of the invention (such transglutaminase activity may be a humanintestinal transglutaminase activity). Typically this is performed byusing a binding assay in which a moiety which binds to the sequence in aspecific manner is contacted with the composition and the formation ofsequence/moiety complex is detected and used to ascertain the presenceof the agent. Such a moiety may be any suitable substance (or type ofsubstance) mentioned herein, and is typically a specific antibody. Anysuitable format of binding assay can be used (such as those mentionedherein).

In one embodiment, the composition is contacted with at least 2, 5, 10or more antibodies which are specific for epitopes of the invention fromdifferent gluten proteins, for example a panel of antibodies capable ofrecognising the combinations of epitopes discussed above in relation toagents of the invention which are a product comprising more than onesubstance.

The composition typically comprises material from a plant that expressesa gluten protein which is capable of causing coeliac disease (forexample any of the gluten proteins or plants mentioned herein). Suchmaterial may be a plant part, such as a harvested product (e.g. seed).The material may be processed products of the plant material (e.g. anysuch product mentioned herein), such as a flour or food that comprisesthe gluten protein. The processing of food material and testing insuitable binding assays is routine, for example as mentioned in Kricka LJ, J. Biolumin. Chemilumin. 13, 189-93 (1998).

Binding Assays

The determination of binding between any two substances mentioned hereinmay be done by measuring a characteristic of either or both substancesthat changes upon binding, such as a spectroscopic change.

The binding assay format may be a ‘band shift’ system. This involvesdetermining whether the presence of one substance (such as a candidatesubstance) advances or retards the progress of the other substanceduring gel electrophoresis.

The format may be a competitive binding method which determines whetherthe one substance is able to inhibit the binding of the other substanceto an agent which is known to bind the other substance, such as aspecific antibody.

Mutant Gluten Proteins

The invention provides a gluten protein in which an epitope sequence ofthe invention, or sequence which can be modified by a transglutaminaseto provide such a sequence has been mutated so that it no longer causes,or is recognised by, a T cell response that recognises the epitope. Inthis context the term recognition refers to the TCR binding the epitopein such a way that normal (not antagonistic) antigen-specific functionalactivity of the T cell occurs.

Methods of identifying equivalent epitopes in other gluten proteins arediscussed above. The wild type of the mutated gluten protein is onewhich causes coeliac disease. Such a mutated gluten protein may havehomology with the wild type of the mutated gluten protein, for exampleto the degree mentioned above (in relation to the analogue) across allof its sequence or across 15, 30, 60, 100 or 200 contiguous amino acidsof its sequence. The sequences of other natural gluten proteins areknown in the art.

The mutated gluten protein will not cause coeliac disease or will causedecreased symptoms of coeliac disease. Typically the mutation decreasesthe ability of the epitope to induce a T cell response. The mutatedepitope may have a decreased binding to HLA-DQ2 or -DQ8, a decreasedability to be presented by an APC or a decreased ability to bind to orto be recognised (i.e. cause antigen-specific functional activity) by Tcells that recognise the agent. The mutated gluten protein or epitopewill therefore show no or reduced recognition in any of the assaysmentioned herein in relation to the diagnostic aspects of the invention.

The mutation may be one or more deletions, additions or substitutions oflength 1 to 3, 4 to 6, 6 to 10, 11 to 15 or more in the epitope, forexample across any of SEQ ID NOS: 1-1927; or across equivalents thereof.Preferably the mutant gluten protein has at least one mutation in thesequence of any of SEQ ID NO: 1-1927. A preferred mutation is at theposition equivalent to position 65 in A-gliadin (see FIG. 10).Preferably, a naturally occurring glutamine is substituted to histidine,tyrosine, tryptophan, lysine, proline, or arginine.

The invention thus also provides use of a mutation (such any of themutations in any of the sequences discussed herein) in an epitope of agluten protein, which epitope is an epitope of the invention, todecrease the ability of the gluten protein to cause coeliac disease.

In one embodiment the mutated sequence is able to act as an antagonist.Thus the invention provides a protein that comprises a sequence which isable to bind to a T cell receptor, which T cell receptor recognises anagent of the invention, and which sequence is able to cause antagonismof a T cell that carries such a T cell receptor.

The invention also provides proteins which are fragments of the abovemutant gluten proteins, which are at least 7 amino acids long (e.g. atleast 8, 9, 10, 11, 12, 13, 14, 15, 30, 60, 100, 150, 200, or 250 aminoacids long) and which comprise the mutations discussed above whichdecrease the ability of the gluten protein to be recognised. Any of themutant proteins (including fragments) mentioned herein may also bepresent in the form of fusion proteins, for example with other glutenproteins or with non-gluten proteins.

The equivalent wild type protein to the mutated gluten protein istypically from a graminaceous monocotyledon, such as a plant of a genusselected from Triticum, Secale, Hordeum, Triticale or Avena, (e.g.wheat, rye, barley, oats or triticale). For example, the protein may bean α, αβ, β, γ or ω gliadin or an avenin.

Kits

The invention also provides a kit for carrying out the method comprisingone or more agents and optionally a means to detect the recognition ofthe agent by the T cell. Typically the different agents are provided forsimultaneous, separate or sequential use. Typically the means to detectrecognition allows or aids detection based on the techniques discussedabove.

Thus the means may allow detection of a substance secreted by the Tcells after recognition. The kit may thus additionally include aspecific binding moiety for the substance, such as an antibody. Themoiety is typically specific for IFN-γ. The moiety is typicallyimmobilised on a solid support. This means that after binding the moietythe substance will remain in the vicinity of the T cell which secretedit. Thus “spots” of substance/moiety complex are formed on the support,each spot representing a T cell which is secreting the substance.Quantifying the spots, and typically comparing against a control, allowsdetermination of recognition of the agent.

The kit may also comprise a means to detect the substance/moietycomplex. A detectable change may occur in the moiety itself afterbinding the substance, such as a colour change. Alternatively a secondmoiety directly or indirectly labelled for detection may be allowed tobind the substance/moiety complex to allow the determination of thespots. As discussed above the second moiety may be specific for thesubstance, but binds a different site on the substance than the firstmoiety.

The immobilised support may be a plate with wells, such as a microtitreplate. Each assay can therefore be carried out in a separate well in theplate.

The kit may additionally comprise medium for the T cells, detectionmoieties or washing buffers to be used in the detection steps. The kitmay additionally comprise reagents suitable for the separation from thesample, such as the separation of PBMCs or T cells from the sample. Thekit may be designed to allow detection of the T cells directly in thesample without requiring any separation of the components of the sample.

The kit may comprise an instrument which allows administration of theagent, such as intradermal or epidermal administration. Typically suchan instrument comprises plaster, dressing or one or more needles. Theinstrument may allow ballistic delivery of the agent. The agent in thekit may be in the form of a pharmaceutical composition.

The kit may also comprise controls, such as positive or negativecontrols. The positive control may allow the detection system to betested. Thus the positive control typically mimics recognition of theagent in any of the above methods. Typically in the kits designed todetermine recognition in vitro the positive control is a cytokine. Inthe kit designed to detect in vivo recognition of the agent the positivecontrol may be antigen to which most individuals should response.

The kit may also comprise a means to take a sample containing T cellsfrom the host, such as a blood sample. The kit may comprise a means toseparate mononuclear cells or T cells from a sample from the host.

Polynucleotides, Cells, Transgenic Mammals and Antibodies

The invention also provides a polynucleotide which is capable ofexpression to provide the agent or mutant gluten proteins. Typically thepolynucleotide is DNA or RNA, and is single or double stranded. Thepolynucleotide will preferably comprise at least 50 bases or base pairs,for example 50 to 100, 100 to 500, 500 to 1000 or 1000 to 2000 or morebases or base pairs. The polynucleotide therefore comprises a sequencewhich encodes the sequence of any of SEQ ID NO: 1-1927 or any of theother agents mentioned herein. To the 5′ and 3′ of this coding sequencethe polynucleotide of the invention has sequence or codons which aredifferent from the sequence or codons 5′ and 3′ to these sequences inthe corresponding gluten protein gene.

5′ and/or 3′ to the sequence encoding the peptide the polynucleotide hascoding or non-coding sequence. Sequence 5′ and/or 3′ to the codingsequence may comprise sequences which aid expression, such astranscription and/or translation, of the sequence encoding the agent.The polynucleotide may be capable of expressing the agent prokaryotic oreukaryotic cell. In one embodiment the polynucleotide is capable ofexpressing the agent in a mammalian cell, such as a human, primate orrodent (e.g. mouse or rat) cell.

A polynucleotide of the invention may hybridise selectively to apolynucleotide that encodes a gluten protein from which the agent isderived at a level significantly above background. Selectivehybridisation is typically achieved using conditions of medium to highstringency (for example 0.03M sodium chloride and 0.03M sodium citrateat from about 50° C. to about 60° C.). However, such hybridisation maybe carried out under any suitable conditions known in the art (seeSambrook et al (1989), Molecular Cloning: A Laboratory Manual). Forexample, if high stringency is required, suitable conditions include0.2×SSC at 60° C. If lower stringency is required, suitable conditionsinclude 2×SSC at 60° C.

Agents or proteins of the invention may be encoded by thepolynucleotides described herein.

The polynucleotide may form or be incorporated into a replicable vector.Such a vector is able to replicate in a suitable cell. The vector may bean expression vector. In such a vector the polynucleotide of theinvention is operably linked to a control sequence which is capable ofproviding for the expression of the polynucleotide. The vector maycontain a selectable marker, such as the ampicillin resistance gene.

The polynucleotide or vector may be present in a cell. Such a cell mayhave been transformed by the polynucleotide or vector. The cell mayexpress the agent. The cell will be chosen to be compatible with thesaid vector and may for example be a prokaryotic (bacterial), yeast,insect or mammalian cell. The polynucleotide or vector may be introducedinto host cells using conventional techniques including calciumphosphate precipitation, DEAE-dextran transfection, or electroporation.

The invention provides processes for the production of the proteins ofthe invention by recombinant means. This may comprise (a) cultivating atransformed cell as defined above under conditions that allow theexpression of the protein; and preferably (b) recovering the expressedpolypeptide. Optionally, the polypeptide may be isolated and/orpurified, by techniques known in the art.

The invention also provides TCRs which recognise (or bind) the agent, orfragments thereof which are capable of such recognition (or binding).These can be present in the any form mentioned herein (e.g. purity)discussed herein in relation to the protein of the invention. Theinvention also provides T cells which express such TCRs which can bepresent in any form (e.g. purity) discussed herein for the cells of theinvention.

The invention also provides monoclonal or polyclonal antibodies whichspecifically recognise the agents (such as any of the epitopes of theinvention) and which recognise the mutant gluten proteins (and typicallywhich do not recognise the equivalent wild-type gluten proteins) of theinvention, and methods of making such antibodies. Antibodies of theinvention bind specifically to these substances of the invention.

For the purposes of this invention, the term “antibody” includesantibody fragments such as Fv, F(ab) and F(ab′)₂ fragments, as well assingle-chain antibodies.

A method for producing a polyclonal antibody comprises immunising asuitable host animal, for example an experimental animal, with theimmunogen and isolating immunoglobulins from the serum. The animal maytherefore be inoculated with the immunogen, blood subsequently removedfrom the animal and the IgG fraction purified. A method for producing amonoclonal antibody comprises immortalising cells which produce thedesired antibody. Hybridoma cells may be produced by fusing spleen cellsfrom an inoculated experimental animal with tumour cells (Kohler andMilstein (1975) Nature 256, 495-497).

An immortalized cell producing the desired antibody may be selected by aconventional procedure. The hybridomas may be grown in culture orinjected intraperitoneally for formation of ascites fluid or into theblood stream of an allogenic host or immunocompromised host. Humanantibody may be prepared by in vitro immunisation of human lymphocytes,followed by transformation of the lymphocytes with Epstein-Barr virus.

For the production of both monoclonal and polyclonal antibodies, theexperimental animal is suitably a goat, rabbit, rat or mouse. Ifdesired, the immunogen may be administered as a conjugate in which theimmunogen is coupled, for example via a side chain of one of the aminoacid residues, to a suitable carrier. The carrier molecule is typicallya physiologically acceptable carrier. The antibody obtained may beisolated and, if desired, purified.

The polynucleotide, agent, protein or antibody of the invention, maycarry a detectable label. Detectable labels which allow detection of thesecreted substance by visual inspection, optionally with the aid of anoptical magnifying means, are preferred. Such a system is typicallybased on an enzyme label which causes colour change in a substrate, forexample alkaline phosphatase causing a colour change in a substrate.Such substrates are commercially available, e.g. from BioRad. Othersuitable labels include other enzymes such as peroxidase, or proteinlabels, such as biotin; or radioisotopes, such as ³²P or ³⁵5. The abovelabels may be detected using known techniques.

Polynucleotides, agents, proteins, antibodies or cells of the inventionmay be in substantially purified form. They may be in substantiallyisolated form, in which case they will generally comprise at least 80%e.g. at least 90, 95, 97 or 99% of the polynucleotide, peptide,antibody, cells or dry mass in the preparation. The polynucleotide,agent, protein or antibody is typically substantially free of othercellular components. The polynucleotide, agent, protein or antibody maybe used in such a substantially isolated, purified or free form in themethod or be present in such forms in the kit.

The invention also provides a transgenic non-human mammal whichexpresses a TCR of the invention. This may be any of the mammalsdiscussed herein (e.g. in relation to the production of the antibody).Preferably the mammal has, or is susceptible, to coeliac disease. Themammal may also express HLA-DQ2 or -DQ8 or HLA-DR3-DQ2 and/or may begiven a diet comprising a gluten protein which causes coeliac disease(e.g. any of the gluten proteins mentioned herein). Thus the mammal mayact as an animal model for coeliac disease.

The invention also provides a method of identifying a product which istherapeutic for coeliac disease comprising administering a candidatesubstance to a mammal of the invention which has, or which issusceptible to, coeliac disease and determining whether substanceprevents or treats coeliac disease in the mammal, the prevention ortreatment of coeliac disease indicating that the substance is atherapeutic product. Such a product may be used to treat or preventcoeliac disease.

The invention provides therapeutic (including prophylactic) agents ordiagnostic substances (the agents, proteins and polynucleotides of theinvention). These substances are formulated for clinical administrationby mixing them with a pharmaceutically acceptable carrier or diluent.For example they can be formulated for topical, parenteral, intravenous,intramuscular, subcutaneous, intraocular, intradermal, epidermal ortransdermal administration. The substances may be mixed with any vehiclewhich is pharmaceutically acceptable and appropriate for the desiredroute of administration. The pharmaceutically carrier or diluent forinjection may be, for example, a sterile or isotonic solution such asWater for Injection or physiological saline, or a carrier particle forballistic delivery.

The dose of the substances may be adjusted according to variousparameters, especially according to the agent used; the age, weight andcondition of the patient to be treated; the mode of administration used;the severity of the condition to be treated; and the required clinicalregimen. As a guide, the amount of substance administered by injectionis suitably from 0.01 mg/kg to 30 mg/kg, preferably from 0.1 mg/kg to 10mg/kg.

The routes of administration and dosages described are intended only asa guide since a skilled practitioner will be able to determine readilythe optimum route of administration and dosage for any particularpatient and condition.

The substances of the invention may thus be used in a method oftreatment of the human or animal body, or in a diagnostic methodpractised on the human body. In particular they may be used in a methodof treating or preventing coeliac disease. The invention also providethe agents for use in a method of manufacture of a medicament fortreating or preventing coeliac disease. Thus the invention provides amethod of preventing or treating coeliac disease comprisingadministering to a human in need thereof a substance of the invention(typically a non-toxic effective amount thereof).

The agent of the invention can be made using standard syntheticchemistry techniques, such as by use of an automated synthesizer. Theagent may be made from a longer polypeptide e.g. a fusion protein, whichpolypeptide typically comprises the sequence of the peptide. The peptidemay be derived from the polypeptide by for example hydrolysing thepolypeptide, such as using a protease; or by physically breaking thepolypeptide. The polynucleotide of the invention can be made usingstandard techniques, such as by using a synthesiser.

Plant Cells and Plants that Express Mutant Gluten Proteins or ExpressProteins Comprising Sequences which can Act as Antagonists

The cell of the invention may be a plant cell, such as a cell of agraminaceous monocotyledonous species. The species may be one whosewild-type form expresses gluten proteins, such as any of the glutenproteins mentioned herein. Such a gluten protein may cause coeliacdisease in humans. The cell may be of wheat, maize, oats, rye, rice,barley, triticale, sorghum, or sugar cane. Typically the cell is of theTriticum genus, such as aestivum, spelta, polonicum or monococcum.

The plant cell of the invention is typically one which does not expressone or more wild-type gluten proteins (such as any of the glutenproteins mentioned herein which may cause coeliac disease), or one whichdoes not express one or more gluten proteins comprising a sequence thatcan be recognised by a T cell that recognises the agent. Thus if thewild-type plant cell did express such a gluten protein then it may beengineered to prevent or reduce the expression of such a gluten proteinor to change the amino acid sequence of the gluten protein so that it nolonger causes coeliac disease (typically by no longer expressing theepitope of the invention).

This can be done for example by introducing mutations into 1, 2, 3 ormore or all of such gluten protein genes in the cell, for example intocoding or non-coding (e.g. promoter regions). Such mutations can be anyof the type or length of mutations discussed herein (e.g., in relationto homologous proteins). The mutations can be introduced in a directedmanner (e.g., using site directed mutagenesis or homologousrecombination techniques) or in a random manner (e.g. using a mutagen,and then typically selecting for mutagenised cells which no longerexpress the gluten protein (or a gluten protein sequence which causescoeliac disease)).

In the case of plants or plant cells that express a protein thatcomprises a sequence able to act as an antagonist such a plant or plantcell may express a wild-type gluten protein (e.g. one which causescoeliac disease). Preferably though the presence of the antagonistsequence will cause reduced coeliac disease symptoms (such as nosymptoms) in an individual who ingests a food comprising protein fromthe plant or plant cell.

The polynucleotide which is present in (or which was transformed into)the plant cell will generally comprise promoter capable of expressingthe mutant gluten protein the plant cell. Depending on the pattern ofexpression desired, the promoter may be constitutive, tissue- orstage-specific; and/or inducible. For example, strong constitutiveexpression in plants can be obtained with the CAMV 35S, Rubisco ssu, orhistone promoters. Also, tissue-specific or stage-specific promoters maybe used to target expression of protein of the invention to particulartissues in a transgenic plant or to particular stages in itsdevelopment. Thus, for example seed-specific, root-specific,leaf-specific, flower-specific etc promoters may be used. Seed-specificpromoters include those described by Dalta et al (Biotechnology Ann.Rev. (1997), 3, pp. 269-296). Particular examples of seed-specificpromoters are napin promoters (EP-A-0 255, 378), phaseolin promoters,glutenine promoters, helianthenine promoters (WO92/17580), albuminpromoters (WO98/45460), oleosin promoters (WO98/45461) and ATS1 and ATS3promoters (WO99/20775).

The cell may be in any form. For example, it may be an isolated cell,e.g. a protoplast, or it may be part of a plant tissue, e.g. a callus,or a tissue excised from a plant, or it may be part of a whole plant.The cell may be of any type (e.g. of any type of plant part). Forexample, an undifferentiated cell, such as a callus cell; or adifferentiated cell, such as a cell of a type found in embryos, pollen,roots, shoots or leaves. Plant parts include roots; shoots; leaves; andparts involved in reproduction, such as pollen, ova, stamens, anthers,petals, sepals and other flower parts.

The invention provides a method of obtaining a transgenic plant cellcomprising transforming a plant cell with a polynucleotide or vector ofthe invention to give a transgenic plant cell. Any suitabletransformation method may be used (in the case of wheat the techniquesdisclosed in Vasil V et al, Biotechnology 10, 667-674 (1992) may beused). Preferred transformation techniques include electroporation ofplant protoplasts and particle bombardment. Transformation may thus giverise to a chimeric tissue or plant in which some cells are transgenicand some are not.

The cell of the invention or thus obtained cell may be regenerated intoa transgenic plant by techniques known in the art. These may involve theuse of plant growth substances such as auxins, giberellins and/orcytokinins to stimulate the growth and/or division of the transgeniccell. Similarly, techniques such as somatic embryogenesis and meristemculture may be used. Regeneration techniques are well known in the artand examples can be found in, e.g. U.S. Pat. No. 4,459,355, U.S. Pat.No. 4,536,475, U.S. Pat. No. 5,464,763, U.S. Pat. No. 5,177,010, U.S.Pat. No. 5,187,073, EP 267,159, EP 604,662, EP 672,752, U.S. Pat. No.4,945,050, U.S. Pat. No. 5,036,006, U.S. Pat. No. 5,100,792, U.S. Pat.No. 5,371,014, U.S. Pat. No. 5,478,744, U.S. Pat. No. 5,179,022, U.S.Pat. No. 5,565,346, U.S. Pat. No. 5,484,956, U.S. Pat. No. 5,508,468,U.S. Pat. No. 5,538,877, U.S. Pat. No. 5,554,798, U.S. Pat. No.5,489,520, U.S. Pat. No. 5,510,318, U.S. Pat. No. 5,204,253, U.S. Pat.No. 5,405,765, EP 442,174, EP 486,233, EP 486,234, EP 539,563, EP674,725, WO91/02071 and WO 95/06128.

In many such techniques, one step is the formation of a callus, i.e. aplant tissue comprising expanding and/or dividing cells. Such calli area further aspect of the invention as are other types of plant cellcultures and plant parts. Thus, for example, the invention providestransgenic plant tissues and parts, including embryos, meristems, seeds,shoots, roots, stems, leaves and flower parts. These may be chimeric inthe sense that some of their cells are cells of the invention and someare not. Transgenic plant parts and tissues, plants and seeds of theinvention may be of any of the plant species mentioned herein.

Regeneration procedures will typically involve the selection oftransformed cells by means of marker genes.

The regeneration step gives rise to a first generation transgenic plant.The invention also provides methods of obtaining transgenic plants offurther generations from this first generation plant. These are known asprogeny transgenic plants. Progeny plants of second, third, fourth,fifth, sixth and further generations may be obtained from the firstgeneration transgenic plant by any means known in the art.

Thus, the invention provides a method of obtaining a transgenic progenyplant comprising obtaining a second-generation transgenic progeny plantfrom a first-generation transgenic plant of the invention, andoptionally obtaining transgenic plants of one or more furthergenerations from the second-generation progeny plant thus obtained.

Progeny plants may be produced from their predecessors of earliergenerations by any known technique. In particular, progeny plants may beproduced by: (a) obtaining a transgenic seed from a transgenic plant ofthe invention belonging to a previous generation, then obtaining atransgenic progeny plant of the invention belonging to a new generationby growing up the transgenic seed; and/or (b) propagating clonally atransgenic plant of the invention belonging to a previous generation togive a transgenic progeny plant of the invention belonging to a newgeneration; and/or (c) crossing a first-generation transgenic plant ofthe invention belonging to a previous generation with another compatibleplant to give a transgenic progeny plant of the invention belonging to anew generation; and optionally (d) obtaining transgenic progeny plantsof one or more further generations from the progeny plant thus obtained.

These techniques may be used in any combination. For example, clonalpropagation and sexual propagation may be used at different points in aprocess that gives rise to a transgenic plant suitable for cultivation.In particular, repetitive back-crossing with a plant taxon withagronomically desirable characteristics may be undertaken. Further stepsof removing cells from a plant and regenerating new plants therefrom mayalso be carried out.

Also, further desirable characteristics may be introduced bytransforming the cells, plant tissues, plants or seeds, at any suitablestage in the above process, to introduce desirable coding sequencesother than the polynucleotides of the invention. This may be carried outby the techniques described herein for the introduction ofpolynucleotides of the invention.

For example, further transgenes may be selected from those coding forother herbicide resistance traits, e.g. tolerance to: Glyphosate (e.g.using an EPSP synthase gene (e.g. EP-A-0,293,358) or a glyphosateoxidoreductase (WO 92/00377) gene); or tolerance to fosametin; adihalobenzonitrile; glufosinate, e.g. using a phosphinothrycin acetyltransferase (PAT) or glutamine synthase gene (cf. EP-A-0,242,236);asulam, e.g. using a dihydropteroate synthase gene (EP-A-0,369,367); ora sulphonylurea, e.g. using an ALS gene); diphenyl ethers such asacifluorfen or oxyfluorfen, e.g. using a protoporphyrogen oxidase gene);an oxadiazole such as oxadiazon; a cyclic imide such as chlorophthalim;a phenyl pyrazole such as TNP, or a phenopylate or carbamate analoguethereof.

Similarly, genes for beneficial properties other than herbicidetolerance may be introduced. For example, genes for insect resistancemay be introduced, notably genes encoding Bacillus thuringiensis (Bt)toxins. Likewise, genes for disease resistance may be introduced, e.g.as in WO91/02701 or WO95/06128.

Typically, a protein of the invention is expressed in a plant of theinvention. Depending on the promoter used, this expression may beconstitutive or inducible. Similarly, it may be tissue- orstage-specific, i.e. directed towards a particular plant tissue (such asany of the tissues mentioned herein) or stage in plant development.

The invention also provides methods of obtaining crop products byharvesting, and optionally processing further, transgenic plants of theinvention. By crop product is meant any useful product obtainable from acrop plant.

Products that Contain Mutant Gluten Proteins or Proteins that CompriseSequence Capable of Acting as an Antagonist

The invention provides a product that comprises the mutant glutenproteins or protein that comprises sequence capable of acting as anantagonist. This is typically derived from or comprise plant parts fromplants mentioned herein which express such proteins. Such a product maybe obtainable directly by harvesting or indirectly, by harvesting andfurther processing the plant of the invention. Directly obtainableproducts include grains. Alternatively, such a product may be obtainableindirectly, by harvesting and further processing. Examples of productsobtainable by further processing are flour or distilled alcoholicbeverages; food products made from directly obtained or furtherprocessed material, e.g. baked products (e.g. bread) made from flour.Typically such food products, which are ingestible and digestible (i.e.non-toxic and of nutrient value) by human individuals.

In the case of food products that comprise the protein which comprisesan antagonist sequence the food product may also comprise the wild-typegluten protein, but preferably the antagonist is able to cause areduction (e.g. completely) in the coeliac disease symptoms after suchfood is ingested.

Deamidation

Where a sequence described herein includes a Gln residue, the inventionalso provides that sequence where the Gln residue has been deamidated toa Glu residue. One or more (e.g., 1, 2, 3, 4, 5, etc.) Gln residue(s)per sequence may be deamidated, but when there is more than one Glnresidue, not all of them must be deamidated. Preferably, the Glnresidues that are deamidated are those susceptible to deamidation bytransglutaminase.

Examples where Gln may be deamidated are given in the sequence listing.For example, residue 4 of SEQ ID NO:1 can be a Gln residue or a Gluresidue, residue 6 of SEQ ID NO:2 can be a Gln residue or a Glu residue,residues 4 and 7 of SEQ ID NO:6 can each independently be Gln or Gluresidues, etc. The Gln residues that are susceptible to deamidation, andtheir deamidated Glu counterparts, are referred to as “Glx” residues.

Where the agent includes more than one Glx residue, these may bearranged in any configuration. For example, the Glx residues may beconsecutive residues, and/or may be separated by one or more (e.g., 1,2, 3, 4, 5, 6, 7, 8, etc.) other residues. As mentioned above, forHLA-DQ8 epitopes, the agent preferably comprises a Glx residue that isseparated by seven residues from another Glx residue.

Preferred agents of the invention are deamidated agents, i.e., the agentcomprises the one or more Glx residues in the Glu form. This can beachieved in various ways, e.g., by including Glu residues duringproduction, or by converting Gln residues to Glu by deamidation.Conversion of Gln to Glu can be achieved by treating an agent thatcontains Gln residues that are susceptible to deamidation with adeamidating agent. The one or more Gln residues are preferablydeamidated to Glu by transglutaminase, for example as described in theexamples. The skilled person will be able to determine which particularGln residues in the agent are susceptible to deamidation and thus whichresidues should be Glu residues arising from deamidation of a Glnresidue. For example, Gln-containing sequences susceptible todeamidation by transglutaminase generally conform to a motif: e.g., QXPX(SEQ ID NO: 1929), QXPF (Y) (SEQ ID NO: 1943), QXX (FYMILVW) (SEQ ID NO:1942), QXPF (SEQ ID NO: 1944), QXX (FY) (SEQ ID NO: 1945), PQ (QL) P(FY) P (SEQ ID NO: 1946). For example, the sequence PQ (QL) P (FY) P(SEQ ID NO: 1946) facilitates deamidation of the underlined Q atposition 2 by transglutaminase.

In particular, agents comprising the deamidated versions of SEQ ID NOs:1-1927 are preferred (where such sequences are not already deamidated).Most preferably, the agents of the invention comprise thetransglutaminase-deamidated versions of SEQ ID NOs: 1-1927 (again, wherenot already deamidated). Analogues and equivalents of these agents, asdefined herein, are also encompassed within the scope of the invention.

EXAMPLES The Invention is Illustrated by the Following NonlimitingExamples: Initial Gliadin Epitope Screening Library

In initial experiments involving 29 HLA-DQ2+ individuals with coeliacdisease on long-term gluten free diet, interferon-gamma ELISPOT assayswere used to screen a previous Pepset (described in WO 03/104273, whichis incorporated herein by reference) initially as pools of peptides andthen in 15 subjects as individual peptides with and without deamidationby tTG.

This Pepset library consisted of 652 20mer gliadin peptides spanning allunique 12mers contained within all Genbank entries described as wheatgliadins found in September 2001. This Pepset library was designed“manually” from gene-derived protein sequences aligned using ClustalWsoftware (MegAlign) arranged into phylogenetic groupings.

Approximately 0.6 micromole of each of 652 of the 20mers was provided.Two marker 20mer peptides were included in each set of 96(VLQQHNIAHGSSQVLQESTY—peptide 161 (SEQ ID NO: 1931), andIKDFHVYFRESRDALWKGPG (SEQ ID NO: 1932)) and were characterized byreverse phase-HPLC and amino acid sequence analysis. Average purities ofthese marker peptides were 19% and 50%, respectively. Peptides wereinitially dissolved in acetonitrile (10%) and Hepes 100 mM to 10 mg/ml.The final concentration of individual peptides incubated with PBMC forthe IFNy ELISpot assays was 20 mcg/ml. These peptides were deamidated byincubation with guinea pig tissue tTG (Sigma T5398) in the ratio 100:32mcg/ml for two hours at 37° C. Peptides solutions were stored at −20° C.and freshly thawed prior to use. These studies were conducted in Oxford,UK. ELlspot assays were performed as described for those conducted inMelbourne, Australia (all other studies described herein). “Oxford” dataregarding subject responses to individual peptides was pooled with“Melbourne” data for subsequent “minimal” epitope analysis in the “EMalgorithm” (see below).

Second Round Gliadin Epitope Screening Library

A second round gliadin epitope library was designed according thebioactive sequences identified from the initial gliadin epitopescreening library of 652 20mers. Gliadin 20mers with mean bioactivityequivalent to >5% of the most potent gliadin 20mer (91:PQPFPPQLPYPQPQLPYPQP (SEQ ID NO: 1933)) in 15 HLA-DQ2+ subjects assessedwith all 652 deamidated 20mers were defined. Since earlier studies (seeWO 03/104273) indicated that deamidated pools of this Pepset were morepotent than without deamidation, glutamine residues within bioactive20mers potentially deamidated by tTG were identified according to themotif QXPX (SEQ ID NO: 1929) , QXZ (FYWILVM) (SEQ ID NO: 1947) where Xis any amino acid except proline, and P is proline, Z is any amino acid,and FYWILVM represent hydrophobic amino acids (consistent with themotifs for tTG-mediated deamidation published by Vader W. et al J ExpMed 2002 J. Exp. Med. 195:643-649, PCT WO 03/066079, and Fleckenstein B.2002. J Biol Chem 277:34109-16).

12mer peptides were then identified in which each potential deamidationsite could be in position 4, 6 or 7 in the 9mer located within HLA-DQ2binding groove (HLA-DQ2 anchors at these positions show a preference forglutamate). Candidate 12mer core epitope sequences were then flankedwith glycine followed by the N-terminal residue present in the parentgliadin polypeptide and at the C-terminal by the C-terminal residuepresent in the parent gliadin polypeptide followed by glycine (i.e.GXXXXXXXQXXXXXXG (SEQ ID NO: 1936)).

Peptides were synthesised with glutamine or glutamate in position 9.Peptides (100 mcg/ml ) (+/−deamidation by tTG) were then assessed ininterferon gamma ELISPOT assays using PBMC from 15 HLA-DQ2+ coeliacvolunteers after gluten challenge. Results of these assays were analysedaccording to the EM algorithm (see below). In addition, the most potentdistinct peptides were synthesised and purified to >80% (Mimotopes) andassessed in interferon gamma ELISPOT assays using PBMC from 15 HLA-DQ2+coeliac volunteers after wheat gluten challenge.

Complete Gluten Epitope Screening Library

To make practical the design of a substantially larger peptide libraryspanning all wheat gliadin and glutenin, rye, barley, and oatgluten-like proteins (prolamines), and to confirm data from the previousgliadin peptide library, an iterative algorithm was developed toautomate design of a minimal set of 20mers including all unique 12mers(excluding signal peptide sequences) in gluten proteins. The ScanSetalgorithm is shown in FIG. 1.

The method tests for all possible peptide epitopes from a group ofproteins whether they are potential antigens in a range of patients.T-cell epitopes range in size between 9 and 15 AA. To test all possible12mers in a set of proteins, becomes quickly unfeasible because of thehigh numbers.

Here we use the fact that, for example, a 20mer peptide can cover up to9 different 12mers. We therefore developed a combinatorial approach tocover all possible 12mers represented in a family of proteins.

20 amino acid (20mer) long peptides are generated that are tested asantigens, and that cover all 12mer peptide sequences that exist in thegroup of proteins. We define the length of peptides to generate as L(e.g. 20) and the length of the epitopes we want to cover as S. Wedeveloped a computer program that generates all uniquely occurring Lmersfrom a set of proteins. Further, we generate all uniquely occurringSmers from this set of proteins. Next we select a set of N Lmers thatcontains all sequences of Lmers. FIG. 1 outlines how this algorithmworks.

On 16 Jun. 2003, Genbank contained accession numbers for 53 alpha/beta,53 gamma and 2 omega gliadins, and 77 LMW and 55 HMW glutenins from T.aestivum, 59 hordeins, 14 secalins, and 20 avenins (see FIG. 2A and FIG.2B). In total, ScanSet identified 18117 unique 12mers contained in the225 gluten gene products.

All unique gluten 12mers could be subsumed in 2922 20mers. These 20merswere synthesised in a Pepset peptide library (Mimotopes Inc., Melbourne,Australia). Pepset peptides were synthesized in batches of 96 (MimotopesInc., Melbourne Australia). Approximately 0.7 to 1.3 micromole of eachof 2922 20mers was provided. Two marker 20mer peptides were included ineach set of 96 (one representative peptide from the 94 other peptides oneach particular plate, and IKDFHVYFRESRDALWKGPG (SEQ ID NO: 1932)) andwere characterized by reverse phase-HPLC and mass spectroscopy. Averagepurities of these marker peptides were 36% (range: 5-68%) and 64%(range:55-71%), respectively.

Peptides were initially dissolved in aqueous acetonitrile (50%).Peptides in aqueous acetontrile were transferred to sterile 96-wellplates and diluted in sterile PBS with 1 mM calcium (250 mcg/ml) andthen incubated with tTG (25 mcg/ml) (Sigma T5398) for 6 h 37° C. andthen stored frozen (−20° C.) until use.

Subjects all had biopsy-proven coeliac disease and had followed a strictgluten free diet for at least 6 months. All subjects possessedHLA-DQB01*02 (HLA-DQ2) alone (n=100) or HLA-DQA1*03 and HLA-DQB1*0302(HLA-DQ8) alone (n=5). In all cases, tTG-IgA was assessed before glutenchallenge and was in the normal range (30% of initial volunteers werefound to have elevated tTG-IgA and were excluded since chronic glutenexposure is associated with failure to induce peripheral bloodgluten-specific T-cells by short-term gluten challenge). Volunteersconsumed Baker's Delight “white bread block loaf” (200 g daily for threedays) or Uncle Toby's oats (100 g daily for three days). All but threesubjects completed the three day challenge (one withdrew after firstmouthful of bread, and the other two vomited after initial two slices ofbread. Data from the latter two were included in subsequent analysis).Blood (300 ml) was drawn six days after commencing gluten challenge.Gluten peptide-specific IFNγ ELISpot responses have not been found inour previous studies, and so “pre-challenge” blood was not assessed inthis set of experiments (Anderson, R P et al 2000. Nat. Med. 6:337-342.,WO 01/25793, WO 03/104273).

IFNγ ELISpot assays (Mabtech, Sweden) were performed in 96-well plates(MAIP S-45, Millipore) in which each well contained 25 mcl of peptidesolution and 100 mcl of PBMC (2−8×10⁵/well) in RPMI containing 10% heatinactivated human AB serum. After development and drying, IFNγ ELISpotplates were assessed using the MAIP automated ELISpot plate counter.Data was then analysed according to a novel algorithm (ExpectationMaximization: EM) to define and quantify interferon-gamma responses to9mer sequences contained within the peptide library (see FIG. 3 andbelow). 9mer peptides were then rationalised according to an algorithmthat assumes redundancy in T-cell recognition, the “IterativeCluster”algorithm (see FIG. 4 and below), by allowing groups of amino acids withsimilar chemical properties at any one position in the 9mer, or forglutamate to replace glutamine at any position (assuming deamidation mayhave occurred).

Since there were data sets from only two HLA-DQ8+ individuals who werenot also HLA-DQ2+, and these were utilizing only the 721 wheat gliadin20mers from the “Complete gluten epitope screening library”, bioactivepeptides were identified by taking the average rank of peptide-specificIFNγ ELISPOT responses in the two subjects. For prediction of likelyHLA-DQ8-restricted gliadin epitopes, it was assumed that a glutamineresidue susceptible to tTG-mediated deamidation occupied either position1 or 9 in potential 9mer core regions of epitopes, consistent with theHLA-DQ8 binding motif and the findings of van de Wal et al (van de Wal,Y. et al 1998. J. Immunol. 161(4):1585-1588).

Expectation Maximization (EM) Algorithm to Analyze Data From ELISpot:

FIG. 3 shows an algorithm to analyze data coming from an assay using theELISpot. T-cell responses to different peptides are measured in 96 wellplates using T-cell assays. Assays are performed on many patients usingmany different peptide antigens. The result of the T-cell assays can besummarized in a table where the rows represent peptides and the columnspatients and the individual measurements (counts) are in the table(e.g., see FIG. 3B). The purpose of the EM algorithm is to differentiatebetween response and non response of a patient to a peptide and toestimate a mean rate of response and a proportion of people respondingfor each peptide.

Responses are measured for a number of different patients (i will beused to indicate the patient) and for many different peptides (j will beused to indicate the peptide). Each measurement (yij) represents a countof T-cells from patient i responding to peptide j. In order to estimate,whether a measurement for a certain peptide in a patient can be called aresponse or whether it is more likely to be coming from a backgrounddistribution, we propose a model for an incomplete data problem, withyij being the observed count of spots and zij an unobserved indicator,whether person i responds to peptide j.

The observed number of counts yij are modelled to come from independentPoisson distributions: poisson(αi, λj), if patient i is responding topeptide j, i.e. zij=1, and poisson(αi, λ0), if patient i is notresponding to peptide j, i.e. zij=0.

-   -   Complete data: yij (observed counts), zij (response indicator,        not observed).    -   Parameters: θ=(αi, λj, λ, pj)        -   αi: Patients overall responsiveness.        -   λj: Peptide induced rate of response.        -   λ0: Background rate of response.        -   pj: Proportion of people responding to peptide j.            EM algorithm:    -   Set variables initially to random values    -   E-step: compute likelihood    -   M-step: maximize likelihood function    -   Iterate E- and M-step

Iterative Procedure to Find Minimal Set of Responsive Epitopes

A program to compute a minimal set of peptides for use in a vaccinebased on the T-cell responses estimated in the EM algorithm wasdeveloped. We measured T-Cell responses to Lmers from a group ofproteins. The peptides were generated to cover all possible Smers. Weestimated the following parameters for the response by an EM algorithm:rate of response, number of people responding, proportion of peopleresponding. The proportion of people responding multiplied with theestimated rate of response is used as a criterion to define epitopeswhich are good antigens. Many of the measured Lmers contain the sameSmer epitopes. In order to find the epitopes (Smers) which can explainall the responses in Lmers we select the Smer which is contained inLmers that in the mean have the highest responses. Then we remove all

Lmers that contain this Smer from our measurements. Next we select theSmer with the highest responses in the remaining Lmers. We iterate thisprocedure until no Smers with responses higher than a specified cutoffexist. We use several iterations with different cutoffs. This process issketched in FIG. 4. The such defined list of clustered Lmers can be usedas a basis to define the optimal epitopes and select peptides thatfunction as good antigens.

HLA-DQ2 Epitopes in Wheat Gluten

HLA-DQ2 epitopes in wheat gliadins and glutenins were identified usingPBMC collected on day 6 after commencing gluten challenge in a total of76 HLA-DQ2+ individuals in gamma-interferon ELISPOT assays (Initialgliadin epitope library: n=15, Second round gliadin epitope screeninglibrary: n=15, Complete gluten epitope screening library: n=46). Alldata relating to individual peptide responses in coeliac subjects waspooled and analysed by the EM algorithm.

A series of 9mer sequences were identified and ordered according to theintensity of gamma-interferon responses and the proportion ofindividuals responding (see FIG. 5A, FIG. 5B, FIG. 5C, FIG. 5D, FIG. 5E,FIG. 5F, FIG. 5G, FIG. 5H, FIG. 5I, FIG. 5J, FIG. 5K, FIG. 5L, FIG. 5M,FIG. 5N, FIG. 5O, FIG. 5P, FIG. 5Q, FIG. 5R, FIG. 5S, FIG. 5T, FIG. 5U,FIG. 5W, FIG. 5V, FIG. 5X, FIG. 5Y, FIG. 5Z, and FIG. 5AA). Many of thesequences identified could be grouped in “superfamilies” allowing forseveral different amino acids with similar chemical properties to bepresent at any one position in the putative epitope (see FIG. 6A, FIG.6B, FIG. 6C, and FIG. 6D). For example, in “Sequence 1” of FIG. 6A (SEQID NO: 1555) P (QR) P (QE) LP (FY) PQ, glutamine (Q) or arginine (R) areboth accepted at position 2 except that Q generates a substantially morebioactive epitope.

By reviewing the 110 most “active” 9mer sequences identified by the EMalgorithm, the “list” of 9mer motifs could be condensed to 41 9mers,many of which overlapped (for example “Sequence 1” and “2” (SEQ ID NOS:1555 and 1558 respectively) overlap by 7 residues and are both presentin A-gliadin 57-73 QE65). In selected cases, high-grade peptides weresynthesised and confirmed the bioactivity of peptides identified by theEM algorithm (see FIG. 7).

HLA-DQ2 Epitopes in Oats Avenins

Avenin peptides were assessed after challenge with oats (n=30 subjects)or after wheat bread (n=8) in HLA-DQ2+ coeliac subjects. ELISPOTresponses were found for the peptides found in FIG. 8. One of thereactive avenin peptides was homologous to a sequence in wheat gluten(SEQ ID NO: 1590).

Oats (Avenin) High Quality Peptide Studies

High grade avenin peptides were assessed 3 days after completing oatschallenge with pure wheat-free oats, 100 g/d for 3 days (“day 6” PBMCinterferon gamma ELISPOT responses). These peptides were designed uponpeptides previously defined using the screening grade (“first round”)avenin peptide library and on potential deamidation sites. There were 25peptides (as 16mers) with purity verified by HPLC as >80%, and sequencesconfirmed by mass spectroscopy.

Interferon gamma ELISPOT responses to the high grade avenin peptidesfollowing deamidation by tTG were compared in 18 subjects with DQ2+coeliac disease.

The dominant (>70% maximal response) peptides after oats challengeincluded: EQQFGQNIFSGFSVQL (SEQ ID NO: 1764) (11/18 subjects),QLRCPAIHSVVQAIIL (SEQ ID NO: 1765) (4/18 subjects), and QYQPYPEQEQPILQQQ(SEQ ID NO: 1766) (3/18 subjects). 2/18 subjects did not have aveninspecific responses (defined by SFU (spot forming units)>3×blank) and6/18 subjects mean maximal SFU were less than 10. Two additionalpeptides elicited positive responses: QIPEQLRCPAIHSVVQ (SEQ ID NO: 1767)(3/18 subjects) and EQYQPEQQPFMQPL (SEQ ID NO: 1768) (>40% maximalpeptide response in 5/18 subjects). The panel of 25 peptides includedseveral peptides similar to peptide 1490 (SEQYQPYPEQQEPFVQ (SEQ ID NO:1948)) reported in Arentz-Hansen, PLoS Medicine (October 2004, vol. 1,issue 1 (84-92), however, that peptide induced a strong positiveresponse in only one subject, and far weaker response in 5 subjects.

Interferon gamma ELISPOT responses to high grade avenin peptides wereabsent prior to gluten challenge, and were blocked by pre-treatment ofPBMC with anti-HLA DQ but not anti-HLA DR antibody.

Rye and Barley Screening Peptide Libraries

Secalin and hordein 20mer first round peptide libraries were assessed 3days after completing rye (bread, 100 g/d for 3 days) or barley (boiled,100 g/d for 3 days) challenge (“day 6” PBMC interferon gamma ELISPOTresponses). Although iterative analysis using 2nd and 3rd round peptidelibraries to define epitopes has not yet been performed, the 20merspre-treated with tTG found to induce “potent” responses sharedsubstantial structural similarity to the bioactive peptides identifiedafter wheat challenge. However, the dominant peptide sequences after ryeor barley challenge did not include peptides with the PQPQLPY sequence(SEQ ID NO : 1937) found to be dominant after wheat challenge. Thedominant (>70% maximal response) 20mer after rye challenge was usuallyPQQLFPLPQQPFPQPQQPFP (SEQ ID NO: 1769) (8/14 subjects), or occasionallyQPFPQPQQPTPIQPQQPFPQ (SEQ ID NO: 1770) (4/14), QQPQQLFPQTQQSSPQQPQQ (SEQID NO: 1771) (1/14), PQTQQPQQPFPQPQQPQQLF (SEQ ID NO: 1772) (1/14)and/or QEQREGVQILLPQSHQQLVG (SEQ ID NO: 1773) (1/14). Additionalpeptides noted for greater than 40% maximal response in at least 1subject include:

(SEQ ID NO: 1774) FPQQPQQPFPQPQQQLPLQP (3/14, 2 > 70%) (SEQ ID NO: 1775)PQQPFPQQPEQIIPQQPQQP (5/14, 3 > 70%) (SEQ ID NO: 1776)QQLPLQPQQPFPQPQQPIPQ (6/14, 2 > 70%) (SEQ ID NO: 1777)QQPQQPFPLQPQQPVPQQPQ (3/14, 1 > 70%) (SEQ ID NO: 1778)SIPQPQQPFPQPQQPFPQSQ (4/14, 1 > 70%) (SEQ ID NO: 1779)QTQQSIPQPQQPFPQPQQPF (3/14, 1 > 70%) (SEQ ID NO: 1780)NMQVGPSGQVEWPQQQPLPQ (2/14, 1 > 70%) (SEQ ID NO: 1781)VGPSGQVSWPQQQPLPQPQQ (2/14, 2 > 70%) (SEQ ID NO: 1782)QQPFLLQPQQPFSQPQQPFL (1/14, 1 > 70%) (SEQ ID NO: 1783)FPLQPQQPFPQQPEQIISQQ (5/14, 1 > 70%) (SEQ ID NO: 1784)PQQPQRPFAQQPEQIISQQP (3/14, 1 > 70%) (SEQ ID NO: 1785)SPQQPQLPFPQPQQPFVVVV (4/14, 1 > 70%) (SEQ ID NO: 1786)QQPSIQLSLQQQLNPCKNVL (1/14, 1 > 70%)

Typically, the dominant peptides after barley challenge included one ofsix peptide motifs, or were one of eight other individual 20mers“dominant” in only one of 17 subjects after barley challenge. The sixmotifs identified:

(SEQ ID NO: 1787) QQPIPQQPQPY (SEQ ID NO: 1788) PFPQPQQPFPW(SEQ ID NO: 1789) LQPQQPFPQ (SEQ ID NO: 1790) PQPQQASPL(SEQ ID NO: 1791) IIPQQPQQPF (SEQ ID NO: 1792) YPEQPQQPF

The barley hordein peptides showing at least 40% maximal peptideresponse in at least one subject include the following, wherein anasterisk indicates the eight individual peptides showing maximalresponse in a single individual:

(SEQ ID NO: 1793) QQQPFPQQPIPQQPQPYPQQ (8/17, 2 > 70%) (SEQ ID NO: 1794)QQPQPFSQQPIPQQPQPYPQ (9/17, 8 > 70%) (SEQ ID NO: 1795)PQQPVPQQPQPYPQQPQPFP (5/17, 1 > 70%) (SEQ ID NO: 1796)PQPFPQQPIPQQPQPYPQQP (6/17, 2 > 70%) (SEQ ID NO: 1797)YPQQPQPFPQQPIPQQPQPY (6/17, 2 > 70%) (SEQ ID NO: 1798)QPQPYPQQPQPYPQQPFQPQ (7/17, 2 > 70%) (SEQ ID NO: 1799)QPQQPQPFPQQPVPQQPQPY (5/17, 2 > 70%) (SEQ ID NO: 1800)PQPYPQQPQPFPQQPPFCQQ (1/17, 1 > 70%)* (SEQ ID NO: 1801)QPFPQPQQPFPWQPQQPFPQ (10/17, 2 > 70%) (SEQ ID NO: 1802)PFPQQPQQPFPQPQQPFRQQ (6/17, 3 > 70%) (SEQ ID NO: 1803)WQPQQPFPQPQQPFPLQPQQ (9/17, 5 > 70%)* (SEQ ID NO: 1804)PWQPQQPFPQPQEPIPQQPQ (1/17, 1 > 70%) (SEQ ID NO: 1805)QQPFPQPQQPIPYQPQQPFN (5/17, 1 > 70%) (SEQ ID NO: 1806)PQQPQQPFPQPQQPFSWQPQ (6/17, 2 > 70%)* (SEQ ID NO: 1807)QPQQPFPQPQQPIPYQPQQP (4/17, 1 > 70%)* (SEQ ID NO: 1808)QSQQQFPQPQQPFPQQPQQP (1/17, 0 > 70%) (SEQ ID NO: 1809)PFPQPQQPFSWQPQQPFLQP (1/17, 0 > 70%) (SEQ ID NO: 1810)FPQPQEPFPQQPQQPFPLQP (1/17, 0 > 70%) (SEQ ID NO: 1811)PFPQPQQPFPWQPQQPFPQP (6/17, 0 > 70%) (SEQ ID NO: 1812)FPQYQIPTPLQPQQPFPQQP (2/17, 1 > 70%) (SEQ ID NO: 1813)FPLQPQQPFPQQPQQPFPQQ (1/17, 0 > 70%) (SEQ ID NO: 1814)QQPFPLQPQQPFPQPQPFPQ (1/17, 0 > 70%) (SEQ ID NO: 1815)SPLQPQQPFPQGSEQIIPQQ (1/17, 0 > 70%) (SEQ ID NO: 1816)PQQASPLQPQPQQASPLQPQ (1/17, 1 > 70%) (SEQ ID NO: 1817)PQQPPFWPQQPFPQQPPFGL (1/17, 1 > 70%)* (SEQ ID NO: 1818)PVLSQQQPCTQDQTPLLQEQ (1/17, 1 > 70%) (SEQ ID NO: 1819)RQLPKYIIPQQPQQPFLLQP (1/17, 1 > 70%) (SEQ ID NO: 1820)QGSEQIIPQQPQQPFPLQPH (7/17, 3 > 70%)* (SEQ ID NO: 1821)PQGSEQIIPQQPFPLQPQPF (2/17, 1 > 70%) (SEQ ID NO: 1822)QPFPTPQQFFPYLPQQTFPP (4/17, 1 > 70%) (SEQ ID NO: 1823)PFPQPPQQKYPEQPQQPFPW (1/17, 1 > 70%) (SEQ ID NO: 1824)QKYPEQPQQPFPWQQPTIQL (1/17, 1 > 70%) (SEQ ID NO: 1825)FQQPQQSYPVQPQQPFPQPQ (3/17, 1 > 70%) (SEQ ID NO: 1826)QIPYVHPSILQQLNPCKVFL (1/17, 1 > 70%) (SEQ ID NO: 1827LAAQLPAMCRLEGGGGLLAS (1/17, 1 > 70%) (SEQ ID NO: 1828)PYLPEELSPQYQIPTPLQPQ (1/17, 1 > 70%)* (SEQ ID NO: 1829)VSPHPGQQTTVSPHQGQQTT (1/17, 1 > 70%)*Second and third round wheat glutenin and gliadin peptide libraries

The second round wheat gliadin and glutenin library was designed uponthe sequences of 20mer wheat gliadin and glutenin peptides that inducedat least 5% of the response (interferon gamma ELISPOT) stimulated by themost active transglutaminase (tTG) pre-treated (enzymaticallydeamidated) 20mer peptide in any subject. All 2nd round 16mer peptideswere assessed in at least 18 subjects. The 2nd round library generatedfrom the “Oxford” gliadin 20mer library had been assessed in tensubjects—this data was merged with data generated from the 18 subjectsused to assess the new 2nd round (expanded) gliadin/glutenin library.Hence, individual 16mer peptides pre-treated with transglutaminase wereassessed in either 18 (novel gliadin/glutenin sequences based on“Melbourne” 20mer library) or 28 subjects (gliadin sequences based on“Oxford” 20mer library). All 16mers identified for the second roundOxford library also fulfilled the selection criteria for the Melbournesecond round library.

The second round peptide library data was analysed according to the“dominance” of peptide responses in the interferon gamma ELISPOT inindividual subjects i.e. the percent response of an individual's PBMC toa specific peptide normalized against that individual's maximalpeptide-induced response. Sequences of peptides that stimulated at least40% of the maximal peptide-specific response in at least one subject areshown in Table 1 below. The dataset supports the consistency and“dominance” of peptides conforming to the sequences identified using thefirst round 20mer peptide library using the Expectation Maximization(EM) algorithm described above.

TABLE 1 Peptides confirmed in Second Round Library as at least40% as active as the peptide with maximal activity in any one subject:Ranked according to potency of peptide family Peptide SEQ ID NO: >70%40-70% 10-40% <10% G-QLPYPQP Q LPYPQP-G 1830 18/28 4/28  3/28  3/28G-LQPFPQPQLPYPQP-G 1831 14/28 8/28 Nil  6/28 G-LQPFPQPQLPFPQP-G 1832 4/28 8/28  5/28 10/28 G-LQPFPQPQLPYLQP-G 1833  1/28 1/28 12/28 14/28G-LQPFPQPQLPYSQP-G 1834  2/28 3/28 12/28 11/28 G-LQPFPQPQLSYSQP-G 1835Nil 1/28  2/28 25/28 G-QQPFPQP Q QPFPWQ-G 1836  9/28 8/28  5/28  6/28G-QQPFPQPQQPIPVQ-G 1837  8/28 5/28  7/28  8/28 G-QQPFPQPQQPFSQQ-G 1838 4/28 7/28  8/28  9/28 G-QQPFPQPQQPFCQQ-G 1839  2/28 2/28 13/28 11/28G-GLERPWQ Q QPLPPQ-G 1840  2/18 1/18 Nil 15/18 G-QTFPHQP Q QAFPQP-G 1841 1/28 2/28 Nil 25/28 LQQQCSPVAMPQRLAR 1842  1/28 1/28 11/28 15/28QGQQGYYPISPQQSGQ 1843  1/18 1/18  1/18 15/18 PGQGQSGYYPTSPQQS 1844  1/181/18 Nil 16/18 QGQPGYYPTSPQQIGQ 1845  1/18 1/18  1/18 15/18GQGQSGYYPTSPQQSG 1846  1/18 Nil  2/18 15/18 QQGYYPTSPQQSGQGQ 1847 Nil1/18 Nil 17/ QGQQGYYPTSPQQPPQ 1848 Nil 1/18 Nil Nil QQGYYPISPQQLGQGQ1849 Nil 1/18 Nil Nil YVPPDCSTINVPYANI 1850  1/18 1/18  1/18 15/18IIMQQEQQEQRQGVQI 1851  1/28 Nil  8/28 19/28 VAHAIIMHQQQQQQQE 1852 Nil1/28  2/28 25/28 G-QPIP Q QP Q QPFPLQ-G 1853  1/28 Nil  5/28 G-FPQLQQP QQPFPQQ-G 1854  1/28 Nil  1/28 26/28 G-FPQTQQPQQPFPQQ-G 1855 Nil 1/28 2/28 25/28 G-QPLSQQPQQTFPQQ-G 1856 Nil 1/28 Nil 27/28G-QQPQQQPQQPFPQQ-G 1857 Nil 1/28  5/28 22/28 G-FPQPQQPQQPFPQQ-G 1858 Nil1/28  3/28 25/28 G-FPQPQQPQQSFPQQ-G 1859 Nil 1/28  1/28 26/28 G-QPQQTFPQ QPQLPF-G 1860  1/18 Nil  2/18 15/18 G-MQVDPSG Q VQWPQQ-G 1861  1/18Nil Nil 17/18 G-IQVDPSGQVQWPQQ-G 1862  1/18 Nil Nil 17/18G-MQADPSGQVQWPQQ-G 1863  1/18 Nil Nil 17/18 G-MQVDPSSQVQWPQQ-G 1864 1/18 Nil Nil 17/18 G-QQEQQIL Q QILQQQ-G 1865  1/18 Nil Nil 17/18VPLYRTTTSVPFGVGT 1866  1/18 Nil Nil 17/18 LQTLPSMCNVYIPPYC 1867  1/18Nil Nil 17/18 LALQTLPAMCNVYIPP 1868  1/18 Nil Nil 17/18 DAIRAIIYSIVLQEQQ1869  1/18 Nil Nil 17/18 G-QQQFSQP Q Q Q FPQP-G 1870 Nil 5/28  7/2816/28 G-FFPQPQQQFPQPQQ-G 1871 Nil 1/28 10/28 17/28 G-FPQQPQQQFPQPQQ-G1872 Nil 1/28 Nil 27/28 G-QQPFPQPQQQFPQP-G 1873 Nil 1/28 12/28 15/28G-QPQPFLP Q LPYPQP-G 1874 Nil 4/28  9/28 15/28 G-QQPFPQP Q QQLPQP-G 1875Nil 3/28  6/28 19/28 G-LPFPQQPQQPLPQP-G 1876 Nil 2/18  4/18 12/18G-QQAFPQP Q QTFPHQ-G 1877 Nil 3/28  8/28 17/28 G-QQPFTQPQQPTPIQ-G 1878Nil 1/28  4/28 23/28 G-QQIFPQPQQTFPHQ-G 1879 Nil 1/28 10/28 17/28G-QQQFIQP Q QPFPQQ-G 1880 Nil 2/28 11/28 15/28 G-QPFPLQPQQPFPQQ-G 1881Nil 2/28  7/28 19/28 G-QPFPWQPQQPFPQQ-G 1882 Nil 2/28  8/28 18/28G-QPTPIQPQQPFPQQ-G 1883 Nil 2/28  5/28 21/28 G-QVSFQQP Q Q Q YPSP-G 1884Nil 2/28  4/28 22/28 G-FFQQPQQQYPSSQQ-G 1885 Nil 1/28  1/28 26/28G-GKSQVLQ Q STYQLL-G 1886 Nil 2/18  1/18 15/18 GQVVNNHGQTVFNDIG 1887 Nil1/18  4/18 G-QPQLPFP Q QPQQQF-G 1888 Nil 1/28  2/28 25/28G-QPFPQPQQAQLPFP-G 1889 Nil 1/28  2/28 25/28 G-HQQPGQR Q QGYYPT-G 1890Nil 1/18  1/18 16/18 G-HQQFP Q Q Q IPVVQP-G 1891 Nil 1/18  1/18 16/18LEAVTSIALRTLPTMC 1892 Nil 1/18  1/18 G-QQPQFSQ Q Q Q IPVI-G 1893 Nil1/18 Nil 17/18

The third round peptide library consisted of 74 peptides based uponstructurally distinct sequences in the second round library found toinduce at least 10% of the maximal response to any peptide in anysubject. These peptides corresponded to wild-type (non-deamidated)sequences virtually identical to those used in the second round library.The distinct feature of this library was that it consisted of peptideswith purity verified by HPLC as >80%, and with sequences confirmed bymass spectroscopy.

Interferon gamma ELSIPOT responses to the 3rd round library peptidesfollowing deamidation by tTG were compared in 14 subjects. Once again,sequences including the PQPQLPY motif (SEQ ID NO: 1937) were “dominant”in 9/14 subjects. However PFPQPQQPFPW (SEQ ID NO: 1894) stimulated >70%of maximal response in 1/14 subjects, PFPQQPQQPFPQ (SEQ ID NO: 1895) in1/14, PQPFLPQLPYPQP (SEQ ID NO: 1896) in 1/14, QPFPQPQQPQQP (SEQ ID NO:1897) in 4/14 (including 3 subjects in whom PQPQLPY peptides (SEQ ID NO:1937) were not potent epitopes) SGQGVSQSQQQSQQQ (SEQ ID NO: 1898) in2/14 (including one in which PQPQLPY peptides (SEQ ID NO: 1937) were notpotent), QYEVIRSLVLRTLPNM (SEQ ID NO: 1899) and GLARSQMLQQSICHVG (SEQ IDNO: 1900) each in one (the same) subject in whom PQPQLPY peptides (SEQID NO: 1937) were not potent epitopes, RTTTSVPFGVGTGVGA (SEQ ID NO:1901) in 1/14 subjects and AIHTVIHSIIMQQEQQ (SEQ ID NO: 1902) in 1/14subjects.

Many of the sequences tested in third round were structurally relatedand individual subject's responses were present or absent according tothe “relatedness” of certain sequences, suggesting redundancy ofpeptides recognized by gluten specific T cells induced by in vivo glutenchallenge.

Interferon gamma ELISPOT responses to 3rd round peptides were absentbefore gluten challenge, and were blocked by pre-treatment of PBMC withanti-HLA DQ but not HLA DR antibody.

Combitopes

The issue of epitope redundancy and the potential utility in diagnosticsand therapeutics of peptides designed to combine “unique” dominantepitopes was addressed by comparing interferon gamma ELISPOT responsesafter wheat (n=16 HLA DQ2 coeliac disease subjects), rye (n=17) orbarley (n=13) challenge to the sequences: QLQPFPQPELPYPQPQL (SEQ ID NO:1903) (“P04724E”), QPEQPFPQPEQPFPWQP (SEQ ID NO: 1904) (“626fEE”), andQLQPFPQPELPYPQPFPQQPEQPFPQPEQPFPWQP (SEQ ID NO: 1905) (“Combitope”).After rye and barley challenge the sum of the median ELISPOT responses(spot forming units) to P04724E and 626fEE were almost identical (99%,and 102%, respectively) to the response to a similar (optimal)concentration of the Combitope. However, after wheat challenge (n=16subjects), median P04724E response was 89% of that to Combitope, andmedian 626fEE responses was 70% of the response to Combitope. Thesefindings would be consistent with substantial redundancy of theserelated epitope sequences, P04724E and 626fEE, after wheat challenge butnot after rye or barley, and that combining dominant epitope sequenceswithin longer peptides does not reduce their biological availability.Hence, combitopes derived from selected potent epitopes may be efficientdelivery devices for T cell epitope-based therapeutics and diagnosticsin coeliac disease.

Epitopes in Wheat Gluten Associated with HLA-DQ8+ Coeliac Disease

Epitopes in wheat gliadins were identified using PBMC after glutenchallenge in two individuals, one HLA-DQ8 homozygous, and one HLA-DQ8heterozygote. Induced T-cell responses in other HLA-DQ8 (not DQ2)coeliac individuals responded weakly to gluten challenge and their datadid not allow detailed analysis.

Deamidated 20mers including the core sequence: QGSFQPSQQ (SEQ ID NO:1906), corresponding to the known HLA-DQ8-restricted alpha-gliadinepitope (in which Q1 and Q9 are deamidated by tTG for optimal activity),induced moderately strong peptide responses. However, a series of “core”peptides were associated with more potent responses in 20mers derivedfrom gamma and omega gliadins (see FIG. 9). The most potent peptidespossessed glutamine in a sequence that would suggest susceptibility todeamidation separated by seven residues from a second glutamine alsosusceptible to deamidation (as found in QGSFQPSQQ (SEQ ID NO: 1906))suggesting that these deamidated sequences would become high affinitybinders for HLA-DQ8 following deamidation by tTG. (The binding motif forHLA-DQ8 favours glutamate at positions 1 and 9.) A further group of20mers possessed glutamine residues susceptible to deamidation but notseparated by seven residues from a second glutamine susceptible totTG-mediated deamidation.

HLA DQ8 Coeliac Disease Gliadin and Glutenin Epitopes

Five subjects with coeliac disease that possess HLA DQ2 and HLA DQ8alleles underwent wheat gluten challenge. PBMC from two subjectsinitially challenged were used to screen the first round “Melbourne”wheat gliadin 20mer library. The 20mer sequences identified using PBMCfrom these two HLA DQ8 CD subjects were dissected further by screening,in five HLA DQ8+ DQ2—CD subjects including the two original subjects, asecond round library based on reactive 20mers in the 1′ round library.The 2_(nd) round library consisted of screening grade overlapping16mers, and 13mers predicted to correspond to tTG-mediated deamidationproducts of epitopes with the potential for deamidation of glutamine atposition 1 and/or position 9 (consistent with the HLA DQ8 peptidebinding motif). In addition, the 1400 glutenin (HMW and LMW)tTG-pretreated 20mers in the “Melbourne” wheat gluten library were alsoscreened in these five subjects.

The most potent and consistently dominant gliadin 16mers were therelated sequences VYIPPYCTIAPFGIFG (SEQ ID NO: 1907) (3/5 subjects >70%response to maximal gliadin 16mer) and AMCNVYIPPYCAMAPF (SEQ ID NO:1908) also dominant in 3/5 subjects (4/5 subjects produced dominantresponses to one or both of these peptides). In addition, a series ofpeptides derived from previously identified bioactive 20mers whoseresponses in the ELISPOT were enhanced or permissive to specificglutamine residues being deamidated were identified: (QE) QPTPIQP (QE)(SEQ ID NO: 1909), (QE) QPFPLQP (QE) (SEQ ID NO: 1910), (QE) QPIPVQP(QE) (SEQ ID NO: 1911), (QE) QPQQPFP (QE) (SEQ ID NO: 1912), (QE) QP(QE) LPFP (QE) (SEQ ID NO: 1913), (QE) GSFQPSQ (QE) (SEQ ID NO: 1914)(previously published HLA DQ8 epitope, van der Wal 1998), (QE) LPFP (QE)QP (QE) (SEQ ID NO: 1915), and (QE)QPFP (QE) QP (QE) (SEQ ID NO: 1916).

Screening the glutenin 20mer library identified a further series ofsequences that were dominant in at least one of the five subjects.Dominant 20mer peptides shared the motifs or had the sequences:PQQQQQQLVQQQ (SEQ ID NO: 1917), QGIFLQPH (LQ) I (AS) QLEV (SEQ ID NO:1918), QPGQGQQG (HY) Y (SEQ ID NO: 1919), QSRYEAIRAII (FY) S (SEQ ID NO:1920), RTTTSVPFD (SEQ ID NO: 1921), QPPFWRQQP (SEQ ID NO: 1922), Q (PS)(PS) (FI) (PS) QQQQ (SEQ ID NO: 1923), (QPLR) GYYPTSPQ (SEQ ID NO: 1924)(previously identified HLA DQ8 epitope, van der Wal 2001), QGSYYPGQASPQ(SEQ ID NO: 1925), GYYPTSSLQPEQGQQGYYPT (SEQ ID NO: 1926), andQGQQLAQGQQGQQPAQVQQG (SEQ ID NO: 1927). Glutenin peptides were assessedafter pre-treatment with transglutaminase. Hence, the requirement fordeamidation for these epitopes is not known.

A comprehensive library of “uncharacterised” screening grade peptidesincluding all unique 12mer sequences encoded by genes present in Genbankdefined as (bread making) wheat (Triticum aestivum), rye, barley, oroats gluten, gliadin, glutenin, secalin, hordein, or avenin have beenassessed using T cells from HLA DQ2+ (and in some cases HLA DQ8+)coeliac disease volunteers six days after commencing in vivo glutenchallenge. A relatively consistent pattern of epitope hierarchy has beenidentified in HLA DQ2 coeliac disease that is similar to but notidentical after consumption of other grains toxic in coeliac disease.Peptides with the sequence PQPQLPY (SEQ ID NO: 1937) are dominant afterwheat challenge in at least two thirds of HLA DQ2+ coeliac disease, butother epitopes are occasionally dominant while PQLPY peptides (SEQ IDNO: 1938) are essentially inactive in fewer than one in six HLA DQ2+subjects with coeliac disease. The contribution of rare dominantepitopes will be better assessed after screening large numbers(e.g. >30) subjects (in progress). Epitope hierarchy after rye andbarley consumption is similar to that after wheat with the exceptionthat deamidated peptides similar to the gliadin/hordein/secalinsequences PQPQQPFP (SEQ ID NO: 1939) or PFPQQPQQP (SEQ ID NO: 1940) areusually dominant rather than PQPQLPY (SEQ ID NO: 1937) (a sequenceunique to wheat alpha-gliadins). Combitopes that comprise serial andpartially overlapping gluten epitopes are as active or more active thansingle epitopes alone and offer a means of efficiently deliveringmultiple gluten epitopes for T cell recognition. Such combitopes aretherefore useful in design and delivery of peptide therapies in coeliacdisease that target multiple unique T cell epitopes.

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11. Arentz-Hansen H, Korner R, Molberg O, Quarsten H, Van der Wal Y,Kooy Y M C, Lundin K E A, Koning F, Roepstorff P, Sollid L M, McAdam SN. The intestinal T cell response to alpha-gliadin in adult celiacdisease is focused on a single deamidated glutamine targeted by tissuetransglutaminase. J Exp Med. 2000; 191:603-12.

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Each of the PCT publications, U.S. patents, other patents, journalreferences, and any other publications cited or referred to herein isincorporated herein by reference in their entirety.

We claim:
 1. A method of preventing or treating coeliac diseasecomprising administering to an individual at least one agent selectedfrom: (a) a peptide comprising at least one epitope comprising asequence selected from the group consisting of SEQ ID NOs: 1-1927, andequivalents thereof; and (b) an analogue of (a) which is capable ofbeing recognised by a T cell receptor that recognises the peptide of (a)and which is not more than 50 amino acids in length.
 2. A method ofclaim 1 wherein the agent is HLA-DQ2-restricted.
 3. A method of claim 1wherein the agent is HLA-DQ8-restricted.
 4. A method of claim 1 whereinone agent is HLA-DQ2-restricted and a second agent isHLA-DQ8-restricted.
 5. A method of claim 1 wherein the agent comprises awheat epitope.
 6. A method of claim 1 wherein the agent comprises an oatepitope.
 7. A method of claim 1 wherein one agent comprises a wheatepitope and one agent comprises an oat epitope.
 8. A method ofpreventing or treating coeliac disease comprising administering to anindividual a pharmaceutical composition comprising an agent as definedin claim 1 and a pharmaceutically acceptable carrier or diluent.
 9. Amethod of preventing or treating coeliac disease comprisingadministering to an individual a pharmaceutical composition comprisingan antagonist of a T cell which has a T cell receptor as defined inclaim 1, and a pharmaceutically acceptable carrier or diluent.
 10. Amethod of preventing or treating coeliac disease comprisingadministering to an individual a composition for tolerising anindividual to a gluten protein to suppress the production of a T cell orantibody response to an agent as defined in claim 1, which compositioncomprises an agent as defined in claim
 1. 11. A method of preventing ortreating coeliac disease comprising: diagnosing coeliac disease in anindividual by either: a) contacting a sample from the host with at leastone agent selected from: i) a peptide comprising at least one epitopecomprising a sequence selected from the group consisting of: SEQ ID NOS:1-1927, and equivalents thereof and ii) an analogue of i) which iscapable of being recognised by a T cell receptor that recognises i) andwhich is not more than 50 amino acids in length; and determining invitro whether T cells in the sample recognise the agent; recognition bythe T cells indicating that the individual has, or is susceptible to,coeliac disease; or b) administering an agent as defined in claim 1 anddetermining in vivo whether T cells in the individual recognise theagent, recognition of the agent indicating that the individual has or issusceptible to coeliac disease; and administering to an individualdiagnosed as having, or being susceptible to, coeliac disease atherapeutic agent for preventing or treating coeliac disease.
 12. Use ofan agent for the preparation of a medicament for treating or preventingcoeliac disease, wherein the agent comprises: (a) a peptide comprisingat least one epitope comprising a sequence selected from the groupconsisting of SEQ ID NOs: 14927 and equivalents thereof; and (b) ananalogue of (a) which is capable of being recognised by a T cellreceptor that recognises the peptide of (a) and which is not more than50 amino acids in length.
 13. A use of claim 12 wherein the agent isHLA-DQ2-restricted.
 14. A use of claim 12 wherein the agent isHLA-DQ8-restricted.
 15. A use of claim 12 wherein one agent isHLA-DQ2-restricted and a second agent is HLA-DQ8-restricted.
 16. A useof claim 12 wherein the agent comprises a wheat epitope.
 17. A use ofclaim 12 wherein the agent comprises an oat epitope.
 18. A use of claim12 wherein one agent comprises a wheat epitope and one agent comprisesan oat epitope.
 19. A use of claim 12 wherein the agent is presentwithin a pharmaceutical composition comprising a pharmaceuticallyacceptable carrier or diluent.
 20. A use of claim 12 wherein the agentis present within a pharmaceutical composition comprising an antagonistof a T cell which has a T cell receptor as defined in claim 12, and apharmaceutically acceptable carrier or diluent.
 21. A use of claim 12wherein the agent is present within a composition for tolerising anindividual to a gluten protein to suppress the production of a T cell orantibody response to an agent as defined in claim
 1. 22. An agent asdefined in claim 1, optionally in association with a carrier, for use ina method of treating or preventing coeliac disease by tolerising T cellswhich recognise the agent.
 23. An antagonist of a T cell which has a Tcell receptor as defined in claim 1, optionally in association with acarrier, for use in a method of treating or preventing coeliac diseaseby antagonising such T cells.
 24. An agent as defined in claim 1 or ananalogue that binds an antibody that binds to an epitope of an agent asdefined in claim 1 for use in a method of treating or preventing coeliacdisease in an individual by tolerising the individual to prevent theproduction of such an antibody.
 25. A protein that comprises a sequencewhich is able to bind to a T cell receptor, which T cell receptorrecognises an agent as defined in claim 1, and which sequence is able tocause antagonism of a T cell that carries such a T cell receptor.
 26. Anagent as defined in claim 1 or an antagonist as defined in claim
 9. 27.A pharmaceutical composition comprising an agent as defined in claim 1or an antagonist as defined in claim 9 and a pharmaceutically acceptablecarrier or diluent.
 28. A composition for tolerising an individual to agluten protein to suppress the production of a T cell or antibodyresponse to an agent as defined in claim 1, which composition comprisesan agent as defined in claim
 1. 29. A composition for antagonising a Tcell response to an agent as defined in claim 1, which compositioncomprises an antagonist as defined in claim
 9. 30. A mutant glutenprotein whose wild-type sequence can be modified by a transglutaminaseto a sequence which is an agent as defined in claim 1, which mutantgluten protein comprises a mutation which prevents its modification by atransglutaminase to a sequence which is an agent as defined in claim 1;or a fragment of such a mutant gluten protein which is at least 7 aminoacids long and which comprises the mutation.
 31. A polynucleotide thatcomprises a coding sequence that encodes a protein or fragment asdefined in claim 25 or
 30. 32. A polynucleotide according to claim 31that additionally comprises one or more regulatory sequences operablylinked to the coding sequence, which regulatory sequences are capable ofsecuring the expression of the coding sequence in a cell.
 33. Apolynucleotide according to claim 32 wherein the regulatory sequence(s)allow expression of the coding sequence in a prokaryotic or mammaliancell.
 34. A polynucleotide according to any one of claims 31 to 33 whichis a vector or which is in the form of a vector.
 35. A cell comprising apolynucleotide as defined in any one of claims 31 to 34 or which hasbeen transformed with such a polynucleotide.
 36. A cell according toclaim 35 which is a prokaryotic cell or a mammalian cell.
 37. A mammalthat expresses a T cell receptor as defined in claim
 1. 38. A method ofdiagnosing coeliac disease, or susceptibility to coeliac disease, in anindividual comprising: (a) contacting a sample from the host with atleast one agent selected from: i) a peptide comprising at least oneepitope comprising a sequence selected from the group consisting of: SEQID NOS: 1-1927, and equivalents thereof; and ii) an analogue of (i)which is capable of being recognised by a T cell receptor thatrecognises (i) and which is not more than 50 amino acids in length; and(b) determining in vitro whether T cells in the sample recognise theagent; recognition by the T cells indicating that the individual has, oris susceptible to, coeliac disease.
 39. Use of an agent as defined inclaim 38 for the preparation of a diagnostic means for use in a methodof diagnosing coeliac disease, or susceptibility to coeliac disease, inan individual, said method comprising determining whether T cells of theindividual recognise the agent, recognition by the T cells indicatingthat the individual has, or is susceptible to, coeliac disease.
 40. Amethod or use according to claim 38 or 39 wherein the agent is ananalogue (iii) which comprises (i) or (ii) bound to (a) an HLA molecule,or (b) a fragment of an HLA molecule capable of binding (i) or (ii). 41.A method or use according to claim 40 wherein the HLA molecule orfragment is in a complex comprising four HLA molecules or fragments ofHLA molecules.
 42. Use according to any one of claims 39-41 wherein themethod comprises administering the agent to the skin of an individualand detecting the presence of inflammation at the site ofadministration, the detection of inflammation indicating that the Tcells of the individual recognise the agent.
 43. A method according toclaim 39, 41 or 42 wherein the sample is blood sample.
 44. A methodaccording to claim 38, 40, 41 or 43 wherein the T cells are notrestimulated in antigen specific manner in vitro before the saiddetermining.
 45. A method or use according to any one claims 38-44 inwhich the recognition of the agent by the T cells is determined bydetecting the secretion of a cytokine from the T cells.
 46. A method oruse according to claim 45 in which the cytokine is IFN-γ.
 47. A methodor use according to claim 45 or claim 46 in which the cytokine isdetected by allowing the cytokine to bind to an immobilised antibodyspecific to the cytokine and then detecting the presence of theantibody/cytokine complex.
 48. A method or use according to any one ofclaims 38 to 44 wherein said determining is done by measuring whetherthe agent binds the T cell receptor.
 49. A method for identifying ananalogue as defined in a claim 38, 40 or 41 comprising determiningwhether a candidate substance is recognised by a T cell receptor thatrecognises an epitope comprising sequence as defined in claim 38,recognition of the substance indicating that the substance is ananalogue.
 50. A method of diagnosing coeliac disease, or susceptibilityto coeliac disease, in an individual comprising determining the presenceof an antibody that binds to an epitope of an epitope comprisingsequence as defined in claim 38 in a sample from the individual, thepresence of the antibody indicating that the individual has, or issusceptible to, coeliac disease.
 51. A method of determining whether acomposition is capable of causing coeliac disease comprising determiningwhether a protein capable of being modified by a transglutaminase to anoligopeptide sequence as defined in claim 38 is present in thecomposition, the presence of the protein indicating that the compositionis capable of causing coeliac disease.
 52. A method according to claim51 wherein the said determining is done by contacting the compositionwith an antibody specific for the sequence which is capable of beingmodified to the oligopeptide sequence, binding of the antibody to aprotein in the composition indicating the composition is capable ofcausing coeliac disease.
 53. A method of identifying an antagonist of aT cell, which T cell recognises an agent as defined in claim 1,comprising contacting a candidate substance with the T cell anddetecting whether the substance causes a decrease in the ability of theT cell to undergo an antigen specific response, the detecting of anysuch decrease in said ability indicating that the substance is anantagonist.
 54. A kit for carrying out a method or use according to anyone of claims 38 to 48 comprising an agent as defined in claim 38, 40 or41 and a means to detect the recognition of the peptide by the T cell.55. A kit according to claim 54 wherein the means to detect recognitioncomprises an antibody to IFN-γ.
 56. A kit according to claim 55 whereinthe antibody is immobilised on a solid support and optionally the kitalso comprises a means to detect the antibody/IFN-γ complex.
 57. Use ofan agent or antagonist as defined in claim 56 or a wild type sequence asdefined in claim 30 to produce an antibody specific to the agent,antagonist or wild type sequence.
 58. Use of a mutation in an epitope ofa gluten protein, which epitope is as defined in claim 38, to decreasethe ability of the gluten protein to cause coeliac disease.
 59. Methodof identifying a product which is therapeutic for coeliac diseasecomprising administering a candidate substance to a mammal as defined inclaim 37 which has, or which is susceptible to, coeliac disease anddetermining whether substance prevents or treats coeliac disease in themammal, the prevention or treatment of coeliac disease indicating thatthe substance is a therapeutic product.
 60. A therapeutic product asidentified in the method of claim 59 for use in a method of preventingor treating coeliac disease.
 61. A method of diagnosing coeliac disease,or susceptibility to coeliac disease in an individual comprisingadministering an agent as defined in claim 38 and determining in vivowhether cells in the individual recognise the agent, recognition of theagent indicating that the individual has or is susceptible to coeliacdisease.
 62. A cell according to claim 35 which is a cell of agraminaceous monocotyledonous species.
 63. A cell according to claim 62which is a cell of wheat, maize, oats, rye, rice, barley, triticale,sorghum, or sugar cane.
 64. A process for the production of a proteinencoded by a coding sequence as defined in claim 31 which processcomprises: (a) cultivating a cell according to any one of claim 35, 36,62 or 63 under conditions that allow the expression of the protein; andoptionally (b) recovering the expressed protein.
 65. A method ofobtaining a transgenic plant cell comprising: (a) transforming a plantcell with a vector according to claim 34 to give a transgenic plantcell.
 66. A method of obtaining a first-generation transgenic plantcomprising: (b) regenerating a transgenic plant cell transformed with avector according to claim 34 to give a transgenic plant.
 67. A method ofobtaining a transgenic plant seed comprising: (c) obtaining a transgenicseed from a transgenic plant obtainable by step (b) of claim
 66. 68. Amethod of obtaining a transgenic progeny plant comprising obtaining asecond-generation transgenic progeny plant from a first-generationtransgenic plant obtainable by a method according to claim 66, andoptionally obtaining transgenic plants of one or more furthergenerations from the second-generation progeny plant thus obtained. 69.A method according to claim 68 comprising: (d) obtaining a transgenicseed from a first-generation transgenic plant obtainable by the methodaccording to claim 67, then obtaining a second-generation transgenicprogeny plant from the transgenic seed; and/or (e) propagating clonallya first-generation transgenic plant obtainable by the method accordingto claim 66 to give a second-generation progeny plant; and/or (f)crossing a first-generation transgenic plant obtainable by a methodaccording to claim 66 with another plant to give a second-generationprogeny plant; and optionally (g) obtaining transgenic progeny plants ofone or more further generations from the second-generation progeny plantthus obtained.
 70. A transgenic plant cell, plant, plant seed or progenyplant obtainable by a method according to any one of claims 65 to 69.71. A transgenic plant or plant seed comprising plant cells according toclaim 62 or
 63. 72. A transgenic plant cell callus comprising plantcells according to claim 62 or 63 obtainable from a transgenic plantcell, first-generation plant, plant seed or progeny as defined in anyone of claims 62, 63, or 65 to
 69. 73. A plant or callus according toany one of claims claim 70 to 72 which is of a species as defined inclaim 62 or
 63. 74. A method of obtaining a crop product comprisingharvesting a crop product from a plant according to any one of claims 70to 73 and optionally further processing the harvested product.
 75. Amethod according to claim 74 wherein the plant is a wheat plant and theharvested crop product is grain; optionally further processed into flouror another grain product.
 76. A crop product obtainable by a methodaccording to claim 74 or
 75. 77. A food that comprises a protein asdefined in any claim 25 or
 30. 78. A food according to claim 77 in whicha protein as defined in claim 25 or 30 is used instead of wild-typegluten.